Dr. Horrible's Sing-Along Blog/WMG

Billy/Dr. Horrible is an AU Severus Snape.
Do I really need to explain this one?

Bad Horse sells out Dr. Horrible for whinnies and giggles.
After Dr. Horrible gets his butt kicked and has a car thrown at his head (in one Captain Hammer Offscreen Moment of Awesome), he speculates that the LAPD and Captain Hammer must watch his blog. Now, the LAPD, maybe--but Captain Hammer? Invincible people don't do research. Besides, Dr. Horrible is just Captain Hammer's punching bag; that "nemesis" title doesn't go both ways. I think it's much more likely that Bad Horse was spying on Dr. Horrible and sent a tip to Captain Hammer and/or the cops. Plenty of reasons that the Thoroughbred of Sin would do this. It could have been a test of his resolve, trying to see if Dr. Horrible is really good enough to be in the ELE. Bad Horse could also have been trying to rub out potential competition, or even just stir up some chaos for fun (since Bad Horse is, by far, the most bloodthirsty character in the show, the first one to suggest killing). If you really want to go far with it, you might even say that Bad Horse set up the whole confrontation at the end, hoping that Dr. Horrible would kill his nemesis, or, better yet, his Designated Love Interest. After all, she was holding him back...

Dr Horrible is dead and in hell.
One of the first things we hear about Bad Horse is his 'Terrible Death Whinny'. During the second Bad Horse Chorus,we actually do hear a horse. This is Bad Horse executing Dr Horrible - over the phone, because, dude, he's Bad Horse! - there is actually no second chance to get into the ELE. Everything after this point is a dead Billy suffering in his own, personal version of hell.

The Evil League of Evil is the beginnings of the Fraternity from the Wanted comic
Dr. Horrible is set before the superhero purge, when villains are just beginning to wise up and group together. Soon, probably with the help of Dr. Horrible, the ELE will launch it's grand campaign to kill or brainwash every superhero in the world. Dr. Horrible becomes a far worse person as villainy becomes the accepted norm, or fully embraces another persona out of guilt, but either way becomes Professor Solomon Seltzer. Captain Hammer had a costume change before the purge, and the cape Seltzer shows Wesley os not actually Superman's cape but Captain Hammer's. Fuckwit is Captain Hammer's imperfect clone that Horrible created as an extra irony of having his archenemy serve him.
 * When I first read the comic, the Fraternity gave me the impression of hating superheroes way more than any DC or Marvel villain ever has hated superheroes...if this WMG is true, then I think I can get why they'd hate them so much, if all superheroes were such assholes, I'd turn into a villain too.

It's all a dream, Dr Horrible is just an insane Youtuber
The only bits that are real are the bits where Dr Horrible is talking to his computer in his room (so not the bit where he says he got a car thrown at his head), and the rest is just wishful thinking. The Evil League of Evil don't exist, Captain Hammer doesn't exist, the death ray doesn't exist at all (you never see it in his blog) and the freeze ray is just a toy.
 * That would explain why at the end the whole thing flashes back to him sitting forlornly in front of his webcam. I choose to believe that the whole plot happens, but without the superpowers- he's just a regular guy whose love interest hooks up with his nemesis. In his imagination it's cooler.
 * And is then murdered by her abusive boyfriend, rather than accidentally killed by an exploding death ray? Actually, a drunk driving accident would be a better parallel in that case...

The Death Ray Worked...
And Billy Buddy is in his own Personal Hell by the end of Act III.
 * The ending is already cruel enough without dragging Hell into it.
 * This theory helps explain how Billy "survived" the explosion that hurt Made of Iron Captain Hammer and killed Penny from across the room without damaging his coat or doing anything else to anyone else. Captain Hammer is a mewling wimp; Dr. Horrible has been inducted into the Evil League of Evil, and he cannot enjoy a moment of it because he's too distraught over Penny's death to gloat.
 * The explosion happened by Hammer's side of the ray, knocking him back. Since he was still holding onto the death ray when he shot it, it flew back with him as some shards exploded across the room (more or less horizontally to the ray), and Billy was "lucky" enough to be under the range of flying shrapnel and exploding ray, as were the hiding innocent bystanders.
 * Maybe Hammer died in the explosion too and they're now sharing the same damnation. Billy loses Penny and Hammer becomes a snivelling mama's boy.

Billy's delusional.
He's hiding away in his basement and is imagining
 * Wait,  Even Evil Has Standards, but why that standard?
 * Point. But then, has led to him becoming introverted and ever-so-slightly crazy and delusional. It wouldn't   damaged him that much mentally that he   Overly-long and elaborate explanation/new part of theory thought up this minute complete.
 * Then again 'introverted and ever-so-slightly crazy' is kind of what you want in a mad scientist...
 * Alternatively,
 * True, but
 * Also, it seems possible that he suffers from multiple personalities: both Dr. Horrible and Billy Buddy refer to each other by name as if they were separate entities, especially at the end of Slipping: "Head up Billy Buddy there's no time for mercy". The final verse of Everything You Ever gives a similar idea: "And now the nightmare is real/Now Dr. Horrible is here".
 * In fact, "Everything You Ever" sounds an awful lot like Dr. Horrible is singing it to Billy.
 * "My victory's complete..." -- Emphasis on the "my." Doc has accomplished his goal, while Billy
 * "And I am fine" may be Doc professing to Billy that while Billy might have the "softer" emotions, Horrible doesn't.
 * "So you think... we all have a choice"-- Billy thought he could change the world, but Horrible is not so naive.
 * "So hail to the king"-- Doc is now the ruler of Billy's mind.
 * Um, wasn't Billy vs. Horrible the main theme of the movie? They diverge around the end of Act II.
 * The two personalities were the same until Billy was taunted by Hammer near the end of Act II, when he became very evil. Then you can see at the end of Act III how Billy is almost completely dead when he finally puts on his goggles, and with the new red-and-evil suit, and how Billy, rather than Dr. Horrible, gives the last word on the blog.
 * It starts off as Dr. Horrible being purely an alias for Billy (so Billy's mind is 90% him, 10% Dr. Horrible); as time goes on, Dr. Horrible manifests himself more and more. Brand New Day was a key turning point, as the two sides of Billy agree with each other: Captain Hammer must die! It also showed Billy throwing away one of his previous qualms (about murder), or rather, Dr. Horrible did it for him (so Billy's mind was approximately 50/50). By the end of Slipping, it's clear that Dr. Horrible is in control, with Billy's nervousness holding him back slightly (25% Billy, 75% Dr. Horrible). Finally, in Everything You Ever, the first 4 lines ("Here lies everything/A world I wanted at my feet/My victory is complete/So hail to the king") are symbolic of Billy's grief about and his anger towards Dr. Horrible (who he holds responsible). However, his next line ("Arise and sing!") is symbolic of his surrender to Dr. Horrible: he knows that there is no redemption for him now, and gives in to his Dr. Horrible persona completely. However, it is also one final command to Dr. Horrible: arise and be all that Billy wanted to be, and more! The rest of the song is Dr. Horrible making his declaration of evil, and a slight explanation of Billy's view of him taking over completely: "And now the nightmare is real/Now Dr. Horrible is here" (Billy, or rather, Dr. Horrible's mind is now 90% Dr. Horrible and 10% Billy). Billy gets the last word of the song, but the room he's in is metaphorical: we see Billy, shell shocked and trapped in his room, but the room is in his, now Dr. Horrible's, mind, having retreated into himself due to his grief.
 * One of the key pieces of symbolism for this is who's doing the blog posting. In the beginning it's Doctor Horrible's blog and he sits behind the webcam making evil plans and glowering at Captain Hammer but his progress is always hampered by the fact that Billy is the one who operates in the real world and despite wearing Dr Horrible's suit to try and attempting to merge these sides of his personality, Billy being the dominant personality always ends up holding back and being unable fully carry out the plans his darker, more eccentric personality concocts. However, after the turning point of Brand New Day and subsequently, the very last words of the blog are up to Billy, sitting in front of his webcam in a plain hoodie completely repressed and powerless while a red suited Dr Horrible has turned the tables and
 * A simpler possible explanation along these lines:
 * Dr Horrible is just a facade; after what he's done, he's got nothing to lose. He's going to rule and change the world, but not in an utopian way like he implied during his first discussion with Penny; it's going to be a nightmare. But Billy is still here; and he's terribly shocked of what he's done, although he doesn't show it to anyone. He's trapped inside Dr Horrible, and he can't show his grief or he won't even have the League.
 * Semi-confirmed by Word of God at the 2008 Comic-con: "Dr. Horrible got what he wanted and Billy lost everything"
 * Not only that, but you could see Billy fighting Horrible during "Slipping" and the showstopper in the middle. The line "Hammer meet nail"? It sounds like Horrible gloating that Hammer has met his match. But what is a hammer's job except to pound a nail into line so that everything doesn't fall apart?
 * He's really bad with analogies? "The snake rots from the head so why not cut off the head?"
 * The FISH.
 * Firstly, this troper interpreted it to be "Hammer me, nail!" This would imply Dr. Horrible gloating that Hammer has been reduced to helplessness. However, this still holds up under the correct lyrics; Horrible is bragging that - as the nail - he has met the Hammer in combat and succeeded.
 * It could be that he's saying "Hammer, meet nail!" as a way of showing Captain Hammer what the metaphorical nail looks like after it's been pounded too much: It snaps.
 * Alternatively, this is the story of Billy Becoming the Mask. Rather than a multiple personality, Dr. Horrible was originally just a character he was playing. To create the kind of social change he desired, he needed a supervillain to make people wake up and let go of their obedient apathy -- notice that as Dr. Horrible, on his blog, he ends his talk about what's wrong with the world with "I just need to rule it" almost tacked on as an afterthought. Billy wants to change the world, but this "Dr. Horrible" character is supposed to be a supervillain, so obviously he should want to rule it. Later, Billy realises that this made-up reasoning is starting to make a lot of sense and that his goals and Dr. Horrible's goals overlap, which (judging by the lyrics of "On The Rise") worries him; that's when he stops playing Dr. Horrible and starts being Dr. Horrible.

The entire show is told through an unreliable narrator in the form of Dr. Horrible.
Clearly, on the blog, someone asked Dr Horrible how he got his start as a villain. The entire story is, to a point, rather self-congratulatory. The villain is clearly noble. A superhero is portrayed as a brainless, brutish thug who also gets his joy out of deliberately and cruelly tormenting the villain.....when no one else is around to hear it. And it goes on. From that last image of the show, we see him finishing his story, which is clear propaganda meant to cast Dr. Horrible in the most sympathetic light possible.

The whole thing is an idea for a story told by a writer-actor on his video blog.
Some of the things outlined in the story are ludicrous, even by supervillain-story standards - for example, a car gets thrown at Dr. Horrible's head and he survives. A lot of things seem to happen in moments that would heighten the drama - Captain Hammer saves the day at the last minute! Captain Hammer enters just as Billy leaves! Billy appears just as Captain Hammer finishes his big song! The large number of Metaphorgottens and Incredibly Lame Puns indicates he's not the most original of writers, and he winds everything up with a Godfather-esque closing of the door to the Evil League of Evil and him, the blogger, singing the final note. And the whole Act III is just one long Creator Breakdown.
 * "Ludicrous, even by supervillain-story standards"? No, "time-honored tropes". There are more ridiculous things in Superman comics, and as you said, it heightens the drama. Superhero comics are full of cheap heightened drama and convenient coincidences. If hero and villain never met, we'd have no story.
 * Tell that to Luc Besson.
 * As for the car throw at the head bit, he said Hammer threw a car at his head; he never claimed that the car hit him. Maybe he dodged and stumbled and, you know, bruised his cheek. Also, the whole stunt falls squarely into the realm of Amusing Injuries and Rule of Funny.
 * Perhaps Dr. Horrible genetically altered himself to have super-resistance to strong blows, which explains how he's survived all of Hammer's punches.
 * Dr. Horrible used the Freeze Ray on the car. Billy's comment about the Freeze Ray taking a few moments to warm up paints a picture of Dr. Horrible cackling, aiming at Captain Hammer, and firing... only for it to produce a buzzing sound long enough for Hammer to throw a car at Horrible, whose ray finally fires, saving him barely... Budgetary constraints, you know.
 * Or Captain Hammer couldn't hit the broad side of a barn. With or without a car.
 * But he DID hit the broad side of a Penny.
 * As for Hammer appearing out of nowhere when Horrible was trying to steal the can with the Wonderflonium, it makes perfect sense: As Dr. Horrible finds out later, Captain Hammer had been viewing Horrible's video blog. We know that he had been blogging about the freeze ray; it's possible that he also mentioned he needed Wonderflonium to power it. Captain Hammer only had to lie in wait to catch him red-handed. It's also possible that the courier van with the Wonderflonium was set up as bait for any aspiring villain in the city, which would explain the lacking security measures; everyone expected Captain Hammer to stop the bad guys.
 * And why Hammer entered the laundromat just when Billy was trying to leave: Penny told Billy that she had told Hammer about her "laundry buddy," and Hammer had expressed a desire to meet him. Given that Horrible had also blogged about Penny extensively (even if he didn't mention or know her name, he may have described her), and that Dr. Horrible was concerned about Penny nearly being run over by the van, it wasn't hard to see the connection. Hammer therefore likely already knew that Billy was Horrible before he even opened his mouth. Just look at him smirk.
 * Billy says 'inadvertantly introduced my arch-nemesis to the girl of my dreams' in his blog just prior to the Bridge Dedication, so it's safe to assume that Captain Hammer knew exactly what Penny was to Billy, anyway.
 * And, um, wasn't Horrible purposefully waiting until Hammer's song was almost done to use his Freeze Ray? He didn't burst in at an opportune moment, he was hiding under the sheet!
 * He was waiting for the freeze ray to charge.
 * How is this different from taking the writers of Dr. Horrible, turning them into one conglomerate character, and criticizing the Blog-- which is fine to do, but since most/all of us here are Horrible fans, you can pretty much see the reaction above?

Captain Hammer is directly responsible for Dr. Horrible's fall to true evil, and thus, the end of the world.
At the end of "Slipping", Dr. Horrible hesitates to kill his arch-nemesis, who has caused him nothing but grief and rubbed it in, despite thinking that Penny isn't watching. Had Captain Hammer not punched Dr. Horrible and fired the exploding death ray, he probably would have backed down. Hammer would beat up Horrible anyway; Penny would see it, really see Hammer for the Jerk Jock he is, and dump him for Billy, who will be caught up in Love Redeems; Hammer would hook up with one of his fangirls, and everyone would live happily ever after.
 * Unless Redemption Equals Death - but even in that case, at least the world in general is better off...
 * ...or Hammer would start brutally beating up Dr. Horrible, and Penny would pick up the death ray and point it at Hammer and tell him "Get lost! Leave us alone" and walk out with Billy. But Joss Whedon never does Happy Endings, and Dr. Horrible wouldn't have acquired the aura of tragedy that every good villain or Anti-Hero needs.
 * Oh, Hammer is definitely responsible. Think about it. Compare Captain Hammer's track record of blithely inflicting bodily harm on people and emotionally torturing Billy, and Hammer's fascist leanings in the comic ("report the freaks to the police"), with Dr. Horrible's deeds. What evil deeds exactly has Horrible committed? His list of crimes comes up as.... theft of gold bars and wonderflonium (it wasn't even a robbery or breaking-and-entering!), and negligible property damage to the ceiling of a public hall. All of Horrible's weapons prior to the death ray were nonlethal. Hell, they were less lethal than a tazer gun! A freeze ray (stops time), a stun ray, and a gun that was supposed to weaken Hammer's muscles (in the comic) but malfunctioned. So we have two cases of pointing (but not firing) nonlethal weapons at a guy who is invulnerable, one case of pointing a potentially lethal death ray at Hammer (but not firing), and one instance of shooting him with a weapon that simply put him in stasis. Horrible has never hurt a living thing; he abhorred killing. There's nothing there that would warrant a death sentence. Hammer, on the other hand, had no compunction about aiming the death ray at Horrible's head and pulling the trigger...
 * This is related, but considering that Captain Hammer goes to Dr. Horrible's blog, he could have been the one to e-mail him asking who "she" was, and thus know exactly who to save.
 * Sure, but Billy never said her name, did he? He doesn't say Penny during the Freeze Ray song.
 * In Captain Hammer's defense, all he saw when he was unfrozen was Dr. Horrible, his arch-nemesis who had reason to kill him, pointing a ray gun at his head. As far as the good captain knew, he had saved himself just in time before being killed. And almost being killed tends to piss most people off.
 * Point, but Hammer had already tried to kill Dr. Horrible at least once by throwing a car at his head -- and in light of that, it's not unreasonable to suspect that he might have been about to kill Horrible even sooner, when he was choking him in front of the van, had Penny's arrival not distracted him.
 * Captain Hammer seemed to enjoy tormenting Dr. Horrible too much to want to kill him, and only seemed ready to do so when Horrible finally started to pose a genuine threat. Granted, this doesn't make Hammer less of a jerkass.
 * Additionally, while it's true that Captain Hammer threw a car at Horrible's head, it's also true that the car missed. Otherwise, Horrible would no longer have a head. It's possible Hammer deliberately missed the throw, and only threw it in the first place to scare him.
 * Another point - the death ray seemed to be working just fine until Captain Hammer became unfrozen. Dr. Horrible fired it into the air several times without blowing it up. The death ray only broke when Captain Hammer punched Dr. Horrible and made him drop it on the floor. Yet another way that Captain Hammer is responsible for the death of Penny.
 * Before the death ray hit the floor, it worked just fine; afterward, the gun was sizzling and crawling with red energy discharges. You can hear and see it. When Hammer points the gun at Horrible, who is lying on the floor, you can see Horrible noticing that something is wrong only after he tilts his head and takes a closer look at the gun (he probably heard the sizzle). That's when his expression changes and he says urgently, "Don't...!" Hammer misinterprets that as "Please don't shoot me!" and cuts him off to gloat, when Horrible was trying to warn him, "Don't fire that, it's overloading!" Since Hammer was previously frozen and had not seen the death ray when it was not broken, he probably thought the red discharges were a feature of the gun.
 * Hammer says "I don't have time for your warnings," almost as if he didn't care that the gun might not work right.
 * Alternate addition: The gun wasn't broken. The gun merely bounced a bit. And what aren't we supposed to bounce?
 * Wonderflonium, true. But Horrible said himself in Act I that the Wonderflonium was for his freeze ray, which remained untouched after powering down, and not his death ray. It just broke when it hit the ground (with the force of a guy who was born able to bench press 500 pounds, remember).
 * But, at the time, he wasn't planning to make a death ray. It's quite possible he did use it in the death ray. But in the end it doesn't really matter does it?

Billy/Dr. Horrible is an Alternate Universe version of Toby from Sweeney Todd: The Demon Barber of Fleet Street
Both were played by Neil Patrick Harris (in the Concert version, that is), both were sweet if slightly neurotic, and both.

Billy can't control which persona is in control
One of Horrible's trademarks (besides the goggles and lab coat) is the squinty expression he gets when annoyed, or happy, or... whenever. But we see Billy get this expression, if only for a split second, at several points -- in the middle of the significant pause when he's talking to Penny and says the power needs "to be put in ... different hands," when Captain Hammer is taunting him, and so on. By "Slipping," Billy is having serious trouble keeping his Dr. Horrible persona in control, but it could be triggered before that. After, the tables are turned; Dr. Horrible usually is active, but Billy pops up from time to time -- hence the ending.

The Fangirls
We know that the Fangirls "have a problem with her". When Captain Horrible fired the malfunctioning Death Ray, they took advantage of the situation and  with some loose shrapnel. When they saw that Captain Hammer had fled the scene but Dr. Horrible cared, they switched loyalties.
 * Why the hell does this make so much sense?
 * Shrapnel flying fast enough to dig into the walls would probably leave a larger wound than the ones Penny had.
 * Devil's advocate - maybe the walls were just really flimsy material? (It's a homeless shelter, who's going to notice and complain? And they got it fixed pretty fast; there could've been some corner-cutting.)
 * Penny's petition at least partly involved taking over an existing building for use as a shelter, IIRC. So the building might be decrepit, but was probably built to code at one time.
 * The fangirls would have to move fast. Weren't they panicking and hiding under chairs?

Penny is
This leaves room for Dr. Horrible to Oh, snap!
 * Seriously, we never She could have just passed out or gone unconscious; we know that the media there isn't particularly reliable, either...
 * One possibility is that  and she will have to face a world where Dr. Horrible is known to be Billy.
 * Commentary! The Musical has so it's not very likely...

He'll get over it.
How well did Billy even know He stalked her from a distance for a while but only knew her in person for a few weeks, at most. He didn't even know her well enough to realize that taking over the world wouldn't win her love. By watching her creepily for so long, he's developed an entirely different personality to associate with her face - simply a fantasy woman who would love him exactly the way he is if he could just be BETTER at who he is. When he hears about her petition, he scoffs at her idea of social change but goes right back into his little act immediately. If he paid closer attention to the real, he'd eventually realize that they just don't fit. Now that she's dead, he'll probably mourn for a while and then attach that fantasy persona to some other girl (one of the fangirls, maybe?). At worst, he'll just build a clone or a robot that'll look like and praise him for everything. At best, he'll accept what has happened and be just fine...well, as fine as a supervillain can be, anyways.
 * Maybe if he'd gotten to know her better, he might have decided they weren't compatible; that's beside the point now. Now that she's dead, she can go on being his ideal fantasy woman in his head without those annoying real personality traits getting in the way. If anything, he's less likely to get over her now that she's dead.
 * Depth and nature of Billy's feelings for aside, there's still the issue that he's at least partially responsible for the death of an innocent person. Even if the loneliness goes away, the guilt will probably linger.
 * See, I interpret it differently. He was attracted to Penny because she represented real goodness in the world he was disillusioned with. His feelings for her were real. He scoffed at her "signatures" because of his cynicism, sure, but he wanted to believe in that kind of goodness. He knew what she was really like, but simply failed to give into the better nature that could embrace it. And he seemed to know, deep down, that taking over the world and doing evil deeds wouldn't really impress her, as evidenced by many of his his lines ("No sign of Penny, good I would give anything not to have her see"). Deep down he knew she wouldn't like what he was doing, and that the path he was taking would probably lead to him not getting the girl ("There's no happy ending, so they say, not for me anyway"). That was sort of the point. Had he not been selfish and let his pride and ambitions get in the way, he could have gotten the girl, he would have gotten the girl. The fact that the woman who represented the idealism he longed for died (and the idealism along with it) is not something that will be easy to overcome, especially since he was indirectly responsible. I imagine it will absolutely HAUNT him.
 * Just a niggle - pretty sure he scoffed at the signatures because he wasn't paying attention. Had to say something to make it sound like he was listening, so he picked any old word to react coolly to. (And the same conversation shows that his idea of being cool is downplaying everything.)
 * But how well could he have known her during the "signatures" conversation when he'd never spoken to her before (seen her from a distance, yes, but never actually talked to her).

Dr. Horrible on purpose.
If the above theories about multiple personalities are true, then the Dr. Horrible persona realized that Penny holds great influence over Billy's ability to suppress Horrible, Incredible Hulk-style. Dr. Horrible intentionally designed the Death Ray to explode if anyone other than Dr. Horrible used it - including Billy. Its shell contained a pair of small smart bombs keyed into Captain Hammer and at least two other targets, if the other conspicuously large bits of shrapnel in the wall are any indication. Dr. Horrible then blocked Billy from understanding how to operate the Freeze Ray, which he could have used to

Dr. Horrible
From how things play out, we see a "zoned out" Billy at the start of the second episode. You know it's Billy and not Dr. Horrible by the look on his face. It is likely that he is starting to rethink his life of crime and is running the scenario of hatred through his head. The conclusion he gets is that "this isn't worth it at all," and he discards the "Doctor Horrible" persona. The sparseness of the lab in the last shot with Billy, the look of abject horror on Billy's face, finally blended with the last words sung and HOW they are presented bring Billy to the horrible (sorry about the pun) revelation of the futility of his situation.
 * What you're saying with this theory is that everything after the beginning of Act II happened in Billy's head. Up until the very end of Act III, where Billy has given up on supervillainy, and being Dr. Horrible, after realizing just how badly things could go. Is this correct?
 * To a "T".
 * It makes more sense to draw the distinction right before he starts singing "Brand New Day" (which, itself being indisputably in his head, effectively means Act III was imagined. . . which is already all over this page).

Billy .
He's really unstable anyway, and Doctor Horrible doesn't seem to care about any of the things Billy does, even joining the Evil League of Evil (he just wants to rule). Based on an idea several guesses above,  The Death Ray only stopped firing forward when it broke, everything else worked exactly the same, and Doctor Horrible tries to stop him not because he's back to Billy and

This is not Dr. Horrible's true Start of Darkness.
That occurred before he got his Ph.D. in Horribleness, when someone kept moving his chair.
 * Does that make Captain Hammer the last surviving Ugliness Man?
 * Well, if you read the article, "start of darkness" is defined as "a Prequel where we find out how the main antagonist from the original story got to that point." Since Doctor Horrible's Sing-A-Long Blog isn't a prequel, it therefore isn't a start of darkness in any case.
 * Well, if you read the article, "start of darkness" is defined as "a Prequel where we find out how the main antagonist from the original story got to that point." Since Doctor Horrible's Sing-A-Long Blog isn't a prequel, it therefore isn't a start of darkness in any case.

The Billy in the final image is Billy's deeper core.
Remember the pie analogy? There's a deeper part of us past our deep part, that is just like what is on the surface. Pie consists of top crust, filling, and bottom crust. In Billy's case the top and bottom crusts are Billy, and the filling is Dr. Horrible.
 * This would mean that he's going to become Billy again in the sequel (it being his true self), possibly via a Morality Pet girl who seems like Penny as a child, a girl whom he desperately wants to ensure does not meet the same fate as Penny. He'll end up fighting not only the Evil League of Evil but Captain Hammer, whose need for therapy drove him to villainy in the frantic search for true invincibility (can't handle pain of any sort, physical or emotional). In the end, he makes a Heroic Sacrifice and thus achieves Redemption; his sacrifice empowers the girl to become a hero in her own right, and she becomes the lead of another strong-female-lead series.
 * However, the Morality Pet girl could also watch Dr. Horrible make his noble sacrifice and blame society for forcing this turn of events, turn inward in a quest for answers, and stumble upon Dr. Horrible's original beliefs, thus spawning a new Dr. Horrible and starting the cycle anew. It mainly depends on whether you prefer European Linear storytelling or Asian Cyclical storytelling.
 * Alternately, the crust is Doctor Horrible. The Billy shown in the final image is a last dribble of Billy left on the bottom crust, after the top crust and filling were scooped out and thrown away once the dead beetle of heartbreak was discovered. The original Doctor Horrible is the top crust, that Billy used to keep from seeming like a completely soft, overly sweet blob of emotion jelly, and the Darker and Edgier Doctor Horrible is the original, bottom crust, which supports the top crust and uses the filling to entice people to accept it, since the bottom crust may be uncomfortably crispier or even unpalatable compared to the lighter, slightly flaky top crust.
 * (Original Poster) Great, now I want some pie.
 * This theory doesn't work, unfortunately. "There's a third, even deeper level, and that one is the same as the top, surface one." If the third, even deeper level, namely Doctor Horrible, differed from the top, surface one, you would not have a pie at all, but a fruit flan. Additionally, the bottom layer of pie is delicious.
 * Actually, it kind of works in a different way: Dr. Horrible is his surface layer, the one he presents to the world -- A horrific villain. The second layer, the filling, is Billy, who is the sweet shy laundry guy. But the dirty layer below that is that Billy is just as horrible as Dr. Horrible is. He stalks Penny, lies to her, masquerades as her friend while hoping to become her lover and is... well, just generally terrible to her. Hell, the more and more I think about it, the more I think Captain Hammer was a better person for her than Dr. Horrible was. (It is, to be fair, a low expectation.) Dr. Horrible is indeed as much the pie as Captain Hammer is. Both have a private side which is, in the end, as much a reflection of their twisted values as their public side.
 * Pumpkin pies don't have a top layer that's the same as the bottom layer. And you know what's cheesy on the outside, and has a bottom layer that's different from the top layer and the filling? Quiche. I don't know what this says abotu Captain Hammer, though.
 * It says he's made of eggs?

Captain Hammer will become an accomplice to Dr. Horrible
After finally feeling pain for the first time, he decides that he never wants to have the feeling again. This is sometime after therapy, and by then, the bad doctor has made a reputation as a supervillain, using his fans as test subjects and such. Hammer turns to Horrible, who performs an experiment that makes him stronger and unable to feel pain. Hammer swears allegiance to Horrible afterwards.
 * Horrible has also made other beings more powerful. He made Moist into a water-based being who changes from solid to liquid form. Since then, Moist is no longer in the henchman's union and is a member of the Evil League of Evil.

In his later years, Dr. Horrible/Billy will build a secret lair on Skullcrusher Mountain
After a while, Billy and Dr. Horrible merge into a single (twisted) persona who tries to replace Penny through supervillainous means and also wants to destroy the world as punishment for taking her away in the first place.

The ending is the start of a Heel Face Turn for Doctor Horrible, who will destroy the Evil League of Evil from within
The fundamental goodness of Penny, so much that she asks Billy if he is okay even while  and doesn't hold any grudge against him, is coupled with   to fundamentally affect Horrible/Billy. The lyrics he sings as he  indicate that Doctor Horrible thinks that Penny believes in a fundamentally good world and that he has inherited it from her. As they cart her away, Billy is choosing to reject the fundamental driving nature of Doctor Horrible while adopting the persona for his own ends. When he enters the League's chamber and sings about making "you quake with fear", he isn't singing to the world, he's singing to the League that he is going to destroy in Penny's name. The final shot of the blog, with Billy wearing his normal clothes, is a sign that Billy has rejected Doctor Horrible. In other words, Billy is about to get Frank Castle on some bitches.
 * Captain Hammer will become scarred and cynical of the real world and, after going through major Character Development, he'll build giant mecha with rollerskates and TAKE OVER THE WORLD.

Billy's plan was the same as the one Angel revealed at the end of the fifth season.
He doesn't want to be a supervillain. That's just a means to an end:  His blog is not 100% truthful, as

Bad Horse is the one of the horses of the apocalypse.
Plague, to be specific. The Evil Germ-Man was his rider before Bad Horse cast him off. The singing cowboys are the other three riders after Bad Horse killed and stole the powers of their horses.

The entire show takes place in the Watchmen universe.
The only way Captain Hammer would be looked at like a paragon of virtue is if he exists in a world where he is that much better than the other heroes. Compared to The Comedian, Ozymandias, Doctor Manhattan and Rorschach, he looks like a paragon.
 * This would also explain Captain Hammer's distrust of "brainy" people if we assume that it's now common knowledge that
 * was never found out. Because of, the Keene Act was withdrawn; the world needed superhuman symbols to rally behind. But to prevent the Superheroes from ever becoming a political issue, the government secretly funded a group of costumed criminals: The Evil League of Evil.
 * He wasn't found out before the story ended. The last panel teases that Ozzy might, in fact, be found out.
 * It might take place in the movieverse, where

Act III takes place in two halves of a forked universe
As per the theories above about one part or the other of Act III being a delusion or a hypothetical. Both of these are true, and the delusion/hypothetical aspects are a residual connection between the halves linking Billy with Dr Horrible. Hey, why not? In Dr Horrible's universe, Penny returns, like in the extensive and elaborate backstory of Donnie Darko. Naturally, this means that Moist will end up tasked with collapsing the tangent timeline. Or something.

Everything in Brand New Day happened, and everything shown after is Dr Horrible speculating on how things would have gone if he hadn't grown himself 50 feet tall
Because somebody needed to say it.

Captain Hammer is from H.A.M.M.E.R.
It explains a lot about his behaviour, and how such a Jerkass would still be considered a Hero makes a lot more sense. Easy to have a good publicity, when H.A.M.M.E.R. pays for it.

Hammer doesn't really have any powers at all.
He's just lucky. And thanks to Love Potion #10, everyone loves him and completely ignores his glaring flaws and Jerkass - ish ways. The only one we ever really see him beating up is Billy, who's probably not that hard to pound on in the first place, being of the geeky scientist type.

That van remote thing? It was light enough to fling across a street so it probably wasn't that durable to begin with, honestly. The gun exploding? Horrible survived unscarred as well and he was just as point blank as Hammer.

And the reason Penny stopped liking Hammer after she started spending time with Horrible? The preventive medicine he had in Horrible Turn could easily have been slipped into Penny's frozen yogurt (or an antidote, since the acid was merely stated to be preventive). Hammers falling out with the public after his defeat could be handwaved with the antidote idea as well. Perhaps a mass produced version Horrible threw in the water main while Hammer was in therapy.


 * Then how did how did he peddle a paddleboat at warp speed, even more important how did he keep it straight?
 * How did he throw a car at Dr. Horrible's head? Remember, Horrible is the one that says it happened. He definitely has powers.
 * In the comic he threw a giant girder, too.
 * Horrible and Hammer both could mentally exaggerate Hammers strength also people all love Hammer so much that they also might exaggerate it as well. It would make more sence for Dr.Horrible to sneak some antidote to Hammerhead when he's recovering. Maby he intentionally forgot about his mistake and during the events came across evidence of it and fixed it first with Penny since he already had a formula for that then Hammer. It would also explain Hammers fangirls switching sides, Wait why am I only drinking as much as I gave to Hammer?

If love potion 10 exists it starts to wear off after 10+ years
If Moist and Wade are not the same person it would have to if Moist would side with Billy over Captain Hammer, and Penny actually was able to have her doupts and might have only bean dating him for simular reasons to why she started dating that one guy in her comic. Billy first encountered Captian Hammer as Dr.Horrible when he was 28, and Billy was under 18 in Horrible turn he should actually be under 15 even if he's a senior. I said starts to it would still partly work.

Captain Hammer Is Cursed
...and the explosion... somehow... broke the curse. Note that the explosion released not only physical pain but emotional pain ("it hurts... in my heart"), neither of which he could previously feel. His inability to connect with girlfriends or sympathize with the down-and-out wasn't a personality flaw; it was a curse that kept him from feeling any sort of pain of any level. (This is somewhat akin to the tale of The Light Princess, who was disconnected from "gravity," such that she floated in the air, but also could not cry and could not take anything seriously; once she learned to love, she also learned to cry and tumbled back to the ground, the curse broken.) Now that he can feel pain, he might be able to sympathize with others (eventually) and thus become a better person.
 * Didn't he say "in my arm"?
 * That would spell the end of the theory... but according to Hulu's closed captioning, Hammer's exact line is, "...in my heart and it hurts..."

Dr. Horrible and Captain Hammer are Brothers.
That would be dramatic.
 * They're more likely half-brothers, though, since Captain Hammer has super powers and Dr. Horrible doesn't.
 * Depends on how Superpowerful Genetics works in that world; Horrible could be a latent recessive carrier, or maybe super-invention is his power.
 * Maybe Horrible got the super-mind, and Hammer got the super-body.
 * Or they both have invulnerability.
 * Dr. Horrible only thinks Captain Hammer didn't get the super mind but Captain Hammer also has his owm... mental capacity. See the comic. hehe capacity nerd.
 * You watch too much TV.

Dr. Horrible and Captain Hammer will hook up.
It would be hot. But then, let's hope the previous WMG isn't true.
 * Hot?? Captain Hammer's inexplicable ability to make people believe he's a great guy seems to work across the divide between fiction and reality, to... urgh.
 * Have you seen Nathan Fillion's ass?? (Firefly episode "Trash.")
 * Exactly.
 * "NPH" would love to brand it.

Bad Horse is the drug dealer in Latawnya the Naughty Horse Learns to Say No to Drugs
Self explanatory. Bad Horse is pure evil.

Captain Hammer was artificially created
Captain Hammer is the product of a government initiative to artificially create superheroes to help fight back against the Dead Bowies and Bad Horses of the world. Why? Because, after getting struck by the exploding death ray, Hammer cries out for "someone maternal". A normal person would cry "Mommy!"/"Mummy!" at the very least; Captain Hammer doesn't because he doesn't have a mother. He could have been grown in some sort of vat or tube. The best he can cry out for is someone vaguely maternal to help him during his first experience of pain. Also, it could explain why he gets away with all the throwing cars around and stuff: The local police have had him assigned to them by the FBI and have to accept that he'll do things like that.
 * Also, his comic on the Dark Horse Myspace Page has him claiming he was born with the ability to bench press five hundred pounds. This sort of child could not be born naturally unless his mother was Supergirl.
 * Also also, in the laundromat, Captain Hammer suggests he's met Billy before at the gym but then realizes he's "naturally this way".
 * It explains his shitty personality. He might be only a couple of years old and have spent all that time being told how great he is by the men who made him. He certainly acts like a kid. “lol, I totally made out with a girl!”
 * He initially calls out "Mama!" "Someone maternal" is said afterwards, presumably after he realized that his mama isn't there.
 * This could also explain why he doesn't seem to have a Secret Identity.
 * Yes he does. What do you think the sweater vests are for?
 * They just are. He can get away with that sort of thing because he is.
 * He definitely doesn't have a secret identity. It's a dry cleaning bill, not the sweater vests themselves, and if you look very closely (if you watch it on HD on a big enough screen, you can read the bill clearly), the name on the bill is "Captain Hammer." And what name do you suppose he signed with the pen that was in his fist? Whether or not he ever had another name, he is obviously legally recognized as "Captain Hammer."

Captain Hammer and Penny were members of the Evil League of Evil
Both of them were sent to masquerade as good people for various reasons, including to test and observe up-and-coming villains such as Doctor Horrible. Captain Hammer being a member is not too subtle, given how much of a Jerkass he is. Penny, on the other hand, was much better as feigning good; however, after Dr. Horrible got the letter from Bad Horse telling him that he will be watched, who are the two people who see him the next day during his heist? Penny's skill at pretending may also have earned her a high position in the league; Dr. Horrible was in a (at least seemingly) high position the moment he was made a member because he managed to kill her. Captain Hammer was kicked out at the end because he was too much of a wimp.

Bad Horse is David Bowie from The Venture Brothers.
He has the power of shapeshifting, and thus can take on the form of a horse. Dead Bowie is a decoy.

Alternately...

Dead Bowie took over the Evil League of Evil...
...renamed it the Guild of Calmonious Intent, and became the Soverign.
 * Nope. Venture Brothers has stated that it was founded in the Victorian Era. Also, Bowie was the Soverign after taking it from Fantômas.

Dead Bowie's superpower is a form of subconscious mind control that manifests itself in dreamlike hallucinations.
"Am I freaking you out, Bret? Is this a freaky dream?"
 * As the world falls down, makes no sense at all, makes no sense to fall...

Bad Horse is trying to destroy the human race.
Notice that in his songs, he seems awfully eager for new members of the Evil League of Evil to prove themselves through murder. Bad Horse's plan is to have them slowly but surely wipe out humanity for him, whereupon he will kill all the members of the League and make horses the rulers of the world.
 * Which clearly ties this in with Gulliver's Travels.
 * Bad Horse being the last living descendant of the Houyhnhnms makes perfect sense: it explains his great intelligence, his powers of speech--plus his general disdain for much of the human race.

Fake Thomas Jefferson isn't fake.
He faked his death to escape debt and then realized he could get away with whatever he wanted because he was supposedly dead. The name is to throw people off so they won't realize he's the real Thomas Jefferson and, subsequently, over two hundred years old.
 * Proven by this video.
 * He says he's the real Thomas Jefferson.

Bad Horse is a political puppet
He's a normal horse, and those singing cowboys who speak for him with absolute authority are the real power behind the Evil League of Evil.
 * But what about his whinny? His terrible Death Whinny!
 * Alternatively, he still is a regular horse, but his henchmen honestly believe that he is a real villain and just consistently misinterpret his behavior and act on what they believe his orders to be.
 * No way; anyone who has ever been around real horses can clearly see their potential for evil.

Bad Horse is Mr. Ed
This should be self-explanatory.

Bad Horse accepted Dr. Horrible
Bad Horse, after coming to the decision that killing was not a true act of evil (just morbid), and after overlooking Dr. Horribles previous grades and realising his potential, was going to send the Bad Horse Chorus over to congratulate him and tell he's in, but they were busy doing something else. So he told one of the Henchmen's Union that he got in, who told Moist, Moist tried to call Dr. Horrible to tell him the news. But he was busy working on a plan to kill Captain Hammer.

Bad Horse is Hammer.
Think about it. You ever seen them in the same place at the same time?
 * We never see him, period. For all we know, Bad Horse is Moist - which would be awesome.
 * Waitaminute... Isn't Bad Horse the horse in the Evil League of Evil at the end???
 * Then that must mean... SHAPESHIFTING is one of Hammer's powers!
 * Or that the horse in the ELE was Fury Leika, and Bad Horse was someone else. It's possible, right?

Bad Horse is a horse.
If Bad Horse was an intelligent horse, it would explain why we haven't seen him - the budget's too low for a talking horse to appear. It would also explain the lame name - "Bad Horse" might be what someone called him before he gained human intelligence.
 * He "whinnies," too. Heh. And it'll probably be a dramatic reveal, anyway.
 * Hey guess what... This one's true. Check the credits.
 * Who didn't see this coming when they called him the "Thoroughbred of Sin"?
 * He is a horse. He's in the last scene, at the head of the Evil League of Evil.
 * Alternately, Bad Horse is a big, skinny donkey. The Evil League of Evils' comic publishers wouldn't let him be called Bad Ass.
 * Because as we all know, evil alliances shy away from mild profanity and puns in their conduct of mass murder and theft, even if it means compromising the title of their independantly established leader.
 * They wouldn't, but their publishers would.

Penny will return in the sequel...as Dr. Horrible's new nemesis
She's so much more heroic than the Jerk Jock Designated Hero Captain Hammer, has elements of The Messiah, so she'd make a good superhero. Bringing her back and making her Billy's mortal enemy would just twist the knife in that much further, fits Joss Whedon's attitude to happy endings perfectly.
 * If that's true, she would need a disguise that she could take off and the end to send him into BSOD. Quite possibly a really good disguise.

Penny is evil.
She's just dating Captain Hammer to infiltrate his secret base and take him out and get into the Evil League of Evil; and Dr. Horrible gets rejected, but they still hook up.
 * Alternatively, Penny is part of the Evil League of Evil as Dr. Horrible's examiner. Dating Captain Hammer (Dr. Horrible's stated nemesis) is just a convenient way of ensuring she's around whenever Dr. Horrible commits his acts of evil.
 * Evidence for Penny being evil: Bad Penny is just too terrible a pun not to use.
 * Well, a bad penny does always come back to you.
 * She's a fellow League hopeful. Her comment about giving homeless people jetpacks to go to the moon wasn't just sarcasm, she was genuinely intrigued and hopeful when Billy slipped and mentioned Bad Horse, and her song's a disguised origin story (she stopped feeling sad and hopeless once she realized the potential of being a supervillain to cause social change.) She was going to tell Billy after the shelter was running and her plan was in play, but, well...
 * She and Dead Bowie could have been Doctor Horrible's testers as in the Laundry Day song there's a poster in his blog called "Dead Not Sleeping" and the fact that Captain Hammer and the LAPD have access to it might mean the League was watching him before sending him the E Lo E request.

Dr. Horrible's true arch-nemesis was never Captain Hammer, and the Evil League Of Evil was aware of this.
Ideologically,  If Captain Hammer had been killed, Billy would have gotten a pat on the back for the good P.R. and a post as Bad Horse's official Hoof-Picker. Unlike Captain Hammer,
 * At least,

This takes place in the same universe as The Middleman.
Think about it: the world is full of low-level weirdoes with a meta sense of humor. Cheap production values further prove this.
 * It helps that the Phased Cannon from "The Palindrome Reversal Palindrome" was the exact same prop as the Freeze Ray.

Penny is Snow White
As long as we're talking about Happily Ever After... Penny's clothes look specially chosen to make her look markedly like Snow White. Ergo... she's, what, Snow White, who didn't get woken by a kiss, but slept in the enchanted slumber until modern days, and was... woken... somehow... quite possibly by someone who was decidedly not Prince Charming, hence her unfulfilling life. She's been expecting Prince Charming and hasn't found him yet - even sings about that - and this provides us with one of two obvious endings:
 * First, by having sex prior to True Love's Kiss, she has broken the magic that enables all Disney heroines to find True Love and live Happily Ever After. Hence, it was ; had she managed to wait around long enough without losing her Virgin Power, she'd be fine and in Billy's arms right now.
 * Yes, except Snow White was originally a German Fairy Tale, of The Brothers Grimm variety. The point is moot anyhow.
 * Second option: No Death by Sex, but she's still waiting for True Love's Kiss to wake her. She might be, in which case some extraordinary efforts will have to be used; else, she's simply comatose (which isn't technically "sleeping"). So this story will be completed in the sequel when Billy finally gives up "everything he's ever wanted" while trying to raise her; finally, in despair of ever undoing the damage he's done, he'll kiss her corpse in final parting (much like a certain current animated movie). This love, for which he has given up money, fame, respect (even self-respect)... this love, which prompted Billy to forsake The Evil League of Evil even on pain of death (so now they're after him, and he's in hiding with Penny's body)... this love which has more than proven its redemptive capabilities will bring Penny back to life. (Heck, X-Men never shied from adding a little magic on top of the super-hero stuff.)
 * And she will wake to find Billy's freshly death-rayed corpse pressed against her lips, as he wanted to go out kissing his One True Love. With the expected result, of course.
 * Unfortunately, Word of God is that the outfit was completely unintentional.
 * Also, there are therapists, though given Captain Hammer's experience with them and the general Crapsack World they're probably incompetent.
 * Damn. I stuck this somewhere else and then came across this Guess and now I feel like I'm dumb for sticking it in the wrong spot to begin with, but here goes: I haven't fully thought this out, which makes me suck, but I think this might be right. The e-mail that leads into 'Freeze Ray' is from someone called dead_not_sleeping. Later, Penny is wearing what essentially amounts to a Snow White costume in the laundromat when she sings her song in the second act. I have no idea what this means, but I feel like it's important. Maybe. Also, hang Word of God. I like this half-baked theory way too much to let it go.

Nobody gets the girl.
Penny is turned off by Dr. Horrible's hubris and Captain Hammer's behavior. Neither man wins her heart, and everyone learns a lesson about being a regular ol' normal person trying to make it in this tough ol' world without black-and-white, Good-and-Evil definitions.
 * Theory confirmed, details Jossed.

We should have seen this ending coming.
WMG is slipping.....
 * Blame it on the Villain Song in Act III for making slipping sound so enticing.
 * Why would you guess it? Considering this is Whedon we're talking about, and Dr. Horrible himself is almost a perfect Captain Ersatz of the three supervillain geeks combined from Buffy the Vampire Slayer, it was a given.
 * He reminds me more of Spike, for all the times when Spike was making Puppy Dog Eyes and was the Butt Monkey of the universe. The tunes of some of Billy's songs resembled Spike's parts in the Buffy musical. And the parallels: Billy = William the Bloody Awful Poet (both were shy and socially awkward around women). Dr. Horrible = Spike the vampire (the cool guy he longs to be, but who always gets upstaged by his nemesis, Hammer/Angel(us), who mocks him and steals his girl, or in Spike's case, girls). Admittedly, Spike has never stalked someone in a laundromat, AFAIK. ;-)
 * It's not wild enough to put here. Just a garden-variety.

Bad Horse got his start when he failed to win the Triple Crown

 * Alternatively, Bad Horse was ALWAYS a bad tempered horse, and the term "bad horse" was repeatedly used by his handlers. When he failed to win the Triple Crown, it was simply his breaking point. He gained his sentience, killed his handler, and went off to a career in villainy, taking the name Bad Horse as both symbolic as his status as a supervillain and an ironic name: his past handlers thought he was bad, and now he's going to prove how right they were! The cowboys are simply a facet of his abilities, an astral projection of himself that manifests as singing cowboys and that can be transmitted via phone signals or used to "charge" inanimate objects (like letters...) so that, when they are received by the intended recipient, the cowboys appear and start singing.
 * That would explain why they're present at the final party...
 * The cowboys were obviously real (notice Moist's reaction when they first turn up), and they are so beholden to Bad Horse that he arbitrarily sends them around to provide singing narration to his correspondence (in the case of the phone call, the phone was silent while the cowboys provided the message) simply because he can.

Bad Horse is Clark Kenting as
Typical for Joss hiding things in plain sight.
 * Wasn't Silver supposed to be...silver?
 * Ah, it's probably just a dye job... it's probably necessary... or at least just wanted... you wouldn't know he was Bad Horse otherwise.

Dr. Horrible's Sing Along Blog is Joss Whedon's attempt at an NGE style Deconstruction of the Super Hero genre.
Think about it, every clichÃ© and standard of the Super Hero genre is either subverted or inverted:
 * Hero is the main character: inverted, the villain is the main character.
 * Hero can survive through anything through strength of character: subverted, Captain Hammer throws himself into every situation heroically, but
 * (then again, this is Joss Whedon we're talking about)
 * Villain is foiled by the hero:
 * Hero is a good and moral person, villain is evil and corrupted: subverted AND inverted - Captain Hammer is a jerk and womaniser, but is still proclaimed as a hero, in a similar way to a Villain with Good Publicity. Dr. Horrible initially has qualms about murdering someone under orders from the Evil League of Evil, but has no qualms about theft. He also cares for Penny, and his key invention is a Freeze Ray which, unlike other villains who would use it for selfish purposes, plans to use it to give him time to speak to Penny without stuttering or mumbling.
 * Hero cares about keeping up the masquerade, villain doesn't: inverted - Captain Hammer is (apparently) Captain Hammer 24/7, whereas Dr. Horrible lives a double life.
 * On the other hand, the sequence of events constitute a perfectly good  origin story for a villain in the superhero genre.
 * This is a WMG? Isn't it a given that it's a deconstruction of the genre?

Dr. Horrible will
What's the point of being a mad scientist if he can't manage a little necromancy?
 * Then there's Moist namedropping a woman called Hourglass, who has some form of time-related powers. Can you think of anybody who might want certain events in his past tweaked?
 * Hourglass seems to be able to see someone's future (she knew that boy would grow up to be a future president) like the protagonist of The Dead Zone, but she must probably meet someone in person for it to work; otherwise, she might have told Moist to warn Dr. Horrible against doing certain things. Which she didn't.
 * Alternatively, he'll get a hold of her body and harvest her eggs. Thus, he'll wind up with an heir that would allow him to at least pretend he'd slept with Penny at some point.

Penny was Blessed with Suck
Twice in the play, malfunctioning technology made a beeline for her. First, the van managed to go straight towards her instead of crashing into anything on the way (like a wall). Next, an explosion defied the laws of physics to hit her with shrapnel. The likeliest explanation is that she has the ability to attract malfunctioning technology, and no knowledge or control over it. Moist demonstrates that superpowers don't have to be particularly impressive in this setting, so if anybody is uncomfortable with the Die for Our Ship situation speculated about above...
 * So Penny is a Walking Techbane and a Butt Monkey?
 * Well, if she has other powers to back it, that power could have been part of a quasi-reasonable set and theme. Give her regeneration, and you get a living crash-test dummy. Some sort of machine-empathy kind of thing, and she could be a Friend To All Machines, with... super-fixing powers, or something. This could be the reason the van stopped right in front of her: once it was that close, repair powers kicked in, and the van started responding to the remote again. Unfortunately, she wasn't close enough to the death ray; the shrapnel accelerated in defiance of logic too much, and the repair powers could conceivably be limited to circuitry. This leads to the slightly odd conclusion that she died because she was too far away from the explosion. Granted, if she'd been closer, Billy would only have lived if she'd moved to stop Captain Hammer.

Penny will return in the sequel.
She will only appear sporadically for a while, causing Dr. Horrible to believe she is a hallucination. She will turn out to be real, but her personality will be a complete reversal of what it had been - bitter, cynical, angsty, and suicidal - though she will seem to possess Penny's memories. It will turn out that  Furthermore,   Of course,
 * Alternatively, Penny returns in the sequel and Billy/Dr. Horrible or Captain Hammer believe her to be real, but she actually IS a hallucination.

Penny never realized that Billy is Dr. Horrible
She never did get a look at the "good" doctor -- remember, she was hiding during the entire master plan -- until she was already dying, at which point, all she sees is his face (completely missing the goggles and labcoat). She never quite makes the connection and thinks Billy was just in the audience for the unveiling of the new shelter. And so, even though she knows that Captain Hammer is a Jerkass, she lies to Billy and tells him that Cap will save them to reassure him. Because Billy is Dr. Horrible, this has the opposite effect and acts to seal his descent into madness.
 * Alternatively, she did realize it (she picked up on the "Head up, Billy buddy" line, after all); but in the shock and trauma of her mortal injury, she can no longer recall anything that's happened over the past quarter hour and so dies believing the integrity of both Billy and Captain Hammer to be unblemished.
 * Assuming she did realize it (which seems likely, given that shot of her mouthing what looks like his name), maybe her last line was so that he wouldn't realize that she knew he was Dr. Horrible. After all, if she heard that whole softer part of "Slipping", she knows that he didn't want her to see him like this, and she makes sure he never knows she figured it out.
 * Before she says "Captain Hammer will save us," she says "Billy? Is that you?".
 * She was near death, and again, had never gotten a real close look at Dr. H; She probably thought Billy was there as a bystander.
 * Alternatively: She did realize that he was Dr. Horrible, and said it to torture him, because he did basically attempt to kill her boyfriend out of jealousy and indirectly result in her death. Maybe she wanted revenge
 * Course, this was after Penny realized Captain Hammer's a big Jerkass.
 * Now that I think about it, maybe it's that she knew Billy was Dr. Horrible, wasn't delusional at all while dying, and was sincerely trying to reassure Billy. She was just being much too idealistic and hoping that Captain Hammer would come back in the room after an epiphany, save her from dying, and save Billy from Dr. Horrible... by "defeating" Dr. Horrible in a way that Billy would no longer keep trying to be that persona and could just be her "Billy buddy". (Either that, or by acting like a real hero for once and not someone Billy feels a need to defeat.) Thus "Captain Hammer will save us" by doing something that will leave them free to be with each other, as themselves.

This is all just a ploy to get tons of money off DVD sales.
Why else would the Whedons take it off the web after only one week?
 * Well, duh. Joss all but said this on the "Master Plan" page on the site.
 * And movies are ...? In fact, you don't even get to see those for free until they're broadcast on TV.
 * And regular TV shows have a much smaller window of opportunity. Until reruns -- and even then you have to stick to the TV schedule (well, unless you record everything).
 * Jossed by Joss himself. Hulu.com has it.
 * Unless you live outside of the USA.
 * No longer on Hulu.

Billy never wore a white lab coat.
For most of the show Billy seems to wear a white lab coat while he's in the "Dr Horrible" persona, changing back into civilian clothes when he's just Billy. Except, in Act I, he ducks behind a wall in normal clothing for a second, then stands up wearing the lab coat. The only explanation is that Billy wears normal clothing at all times - the lab coat is just a visual representation of his state of mind. Even the red coat at the end could be imaginary in the same way.
 * Doesn't work. Even if Captain Hammer recognized him right away, waiting for Penny to leave the room first suggests that he knows Penny is oblivious to Billy's supervillain identity.
 * Sure? Even if Penny did know, or Captain Hammer thought she knew, Captain Hammer did say some things that he probably didn't want his girlfriend to overhear.
 * Ah, but in the supplemental comics from Moist and Hammer's perspectives, the good doctor's still in the lab coat.

Two days after the last images of the show, Billy commits suicide

 * Then how is there going to be a sequel?
 * Well, that wouldn't necessarily be a problem. But really... there shouldn't be a sequel.
 * Agreed. No matter how much we like the character, some stories are... complete in themselves. They are cheapened by sequels.
 * How would it be cheapened? Using a sequel to further twist the knife in and show a "true Villain" Dr. Horrible struggling to cope with his dark world after the death of Penny? How would that cheapen it? Besides, Joss himself has said repeatedly he would love to do a sequel/there will be a sequel. He's even implied he already has a story in mind. One of the reasons they haven't begun work on it yet is because Joss is working on Dollhouse, and Neil has a full-time gig on How I Met Your Mother. But they have all expressed interest in it.
 * Why two days? Just out of interest.
 * His situation needs some time to sink in. The first few days, he just gets swept up by the whole new Evil League of Evil thing, robbing banks, etc., other villains cheering him on. It stops him from thinking about what happened. But once the first excitement is over and Billy faces days (or nights, it's night in the last shot) full of emptiness and despair, walking the city streets, passing by the laundromat where she won't be waiting for him, never again... how long do you think he will last? If he makes it past the first few months, then he'll probably live because he has managed to return to some semblance of normalcy. Or "Billy" as we know him will disappear completely as he commits symbolic suicide by utterly embracing the Dr. Horrible persona and never ever looking back. But even supervillains have to go to sleep. Brush his teeth, eat breakfast, watch as some henchman does his laundry for him...

Captain Hammer's penis is a hammer
This was why Penny was really getting distant from Captain Hammer.
 * He does seem the kind of guy who might... name his superheroic pseudonym after his junk.
 * What sort of hammer is it, though?
 * Claw hammer, if his chest insignia is any indication...
 * Ball-peen is funnier.
 * Nathan Fillion said it was a ball-peen hammer at a Dragon* Con panel.
 * This perfectly explains why Captain Hammer has never slept with the same girl twice.
 * Wouldn't even the first time qualify as "the weird stuff" in this case?
 * Confirmed: "It is actually shaped like a little hammer... well, little for a hammer."

Doctor Horrible became a supervillain because everyone expected him to.
He lives in a world where exceptional students in science are reported to the police for surveillance.
 * Look at what the world is okay with accepting as a hero. If that's their idea of a hero, he couldn't go that route.
 * The public police-state-like prejudice against scientists and engineers might even be the reason Billy seems to have no job! He's a brilliant gadgeteer (he can build rayguns that freeze time!); but he has to go to the laundromat to get his clothes washed, so he's probably poor, and he shares an apartment with Moist. Don't ask where he gets the parts for all the gadgets he designs if he is poor... perhaps he steals them, just as he stole the Wonderflonium? Perhaps he used to have more income in the past? Perhaps he's using up an inheritance from his dead parents? In comic books, supervillains and superheroes are either filthy rich or have just enough mysterious sources of income to get along (unless they're called Spiderman) and have access to technical gadgets even if they're living in the sewers. It's just one of those things.
 * Billy's whole attitude is a mixture of extreme shyness and bitterness and frustration, like someone who has been beaten up by life so often that he has withdrawn into himself. Normally, you would expect someone like him to be courted by corporate and military headhunters and offered vast sums of money to design weapons. Billy is an anarchist and revolutionary at heart, not to mention a pacifist; maybe he declined those offers and lost his job. Another reason he is bitter. He wants people to acknowledge his genius, but instead they're all cheering for a smarmy jerk who lives on government funding (the Hammercycle, the Ham-jet).
 * I think his true "shift" into real villany was when penny told him "Captain Hammer will save us" His crowning moment was kicked out from under him because of his weakness to kill his arch, the arch takes his gun, ignores his warnings, and causes the death of the girl he loves, the girl who 'refuses to to see Hammer for what he really is even after his antics caused her death' And what does she say as she's dieing? "Captain Hammer will save us" Save you?! He's killed you! * I* was going to save you! I was going to save the WORLD! But no... I see now that the world is too blind to save... * Cue red coat*
 * Or, just throwing this out here, he doesn't have a job because he's publicly plotting to take over the world.
 * Is there a chance that Dr. Horrible's last name is actually Horrible? That's got to limit your career options.
 * Nope. It's Buddy. It's in the credits, and also mentioned in Slipping.
 * Is it? I'm pretty sure on the cast list the character's identified as "Dr. Horrible" with no reference to his given name, first or last.
 * I've just read through the entire credits; nowhere is the character referred to as anything other than "Dr. Horrible". However, this blogger makes a good case for the name being a reference to Melville's "Billy Budd", which points to "Billy Buddy" being the character's full name. None of the writers or cast appear to have made any statements one way or the other at this point.
 * Penny tells Billy to "keep your head up, Billy buddy". This is the reason for the "head up Billy buddy" line in Slipping -- Penny encouraged him to keep going and strive for his goal (not knowing what the goal was, of course) when going for the "job" he was trying to get.
 * The "Billy Buddy" thing is Penny's nickname for him.

Captain Hammer will become Mal Reynolds
After experiencing pain he becomes slightly more humble and retires, but is still a bit of a jackass. Due to his superhuman nature, he outlives all memory of his being a Superhero, and he fights against the Alliance during the war to redeem himself...and well, this one needs to be said.
 * Fuck Yeah!
 * Instead of just retiring, he becomes a pro-Muggle political crusader with a strong dislike of anyone who meddles with normal folk. His anti-super efforts are so successful that by the twenty-sixth century people with strange powers are considered witches once again.
 * Alternatively, the entire thing was a Show Within a Show in the Firefly Verse (as per the hacking of the Emmys; see, Penny's there!) and a younger, more innocent/stupid Mal agreed to play the part for some easy cash. And I'm not the only one who thinks so.
 * Adding to this theory, Simon and River Tam are descendants of Billy. The lab coat Simon uses in Ariel was passed down from his ancestor Dr. Horrible back on Earth-that-was. Billy was an inventor and thus, we can guess, pretty smart, which stayed in their genes and reappeared in the Tam siblings. Mal recognizes Simon's heritage at the beginning of the show (though, having forgotten his stint as Captain Hammer, can't quite put his finger on why he hates Simon so much) which results in the initial animosity between the two characters.

Captain Hammer will become Caleb
The First Evil was empowering him from birth. Once he gets over the pain, he'll don the priestly collar and go after Buffy.
 * Alternatively, Captain Hammer was super strong from some other source, then, faced with his own apparent mortality, joins the legitimate priesthood to protect his immortal soul, but is later approached by the First Evil and offered a more violent path to "immortality" -- the First's power ups.

Captain Hammer will become the Commander.
After recovering from his humiliating defeat, Hammer reforms and goes back to being a superhero, with a new name: the Commander (who has a cape, see below.) He becomes well-loved once more, and then ends up settling down with Jetstream to have Will.

Their powers are basically the same, so it's not too much of a stretch. As well, he might take the name Commander to help himself recover from his humiliation, signifying that he's now "in command" of everything in his life.

The entire show is a Deconstruction of Cannot Spit It Out.
Billy suffers from a common hero affliction -- he can't tell the girl he loves how he feels about her. In a "straight" example, the hero tells the girl he loves about his feelings near the end, and they defeat the bad guys and live happily ever after. In Dr. Horrible, Billy ends up indirectly killing the girl he loves without ever letting her know how he felt despite her obviously liking him, and it all could've been avoided if he'd asked her out for frozen yoghurt during the first song.
 * It would have been avoided; Penny was waiting for Billy at the laundromat and doubting her relationship with Captain Hammer ("This is perfect for me - So they say/I guess he's pretty okay...") in "So They Say". If Dr. Horrible didn't get whipped up into a frenzy and start plotting Hammer's death, he would have got the girl, no problem.
 * It would have been avoided even before that! If Billy had stopped fiddling with the remote control for the van, ignored the whole Wonderflonium heist idea, scrapped the freeze ray plans, and said: "Gee Penny, I really am interested in this homeless shelter idea of yours! Tell me more!", they'd both be living happily ever after by now. (If they also hadn't both had the misfortune of being in a Joss Whedon production, that is)
 * Until the ELE kills them. The lines "this grade will be your last" and "there will be blood, it might be yours" in Bad Horse's songs might have darker meanings.

After his humiliating public defeat, Captain Hammer becomes the next member of the Evil League of Evil
Hammer's reputation is shot to pieces. The media will look for a new "hero" while Hammer is in therapy. Even if Hammer tries to return to his role, he'll never dare antagonize Dr. Horrible for fear of what Horrible will do next. Cut off from the government honey pot, Captain Hammer decides to turn to a life of crime, where he can do what he loves best (beating people up). He sends his application to the Evil League of Evil, commits some atrocities, and is accepted almost instantly, which will piss Dr. Horrible off big time. Once he is part of the League, Hammer starts intimidating and upstaging Dr. Horrible again because Hammer has a natural talent for being a jerk. The rest of the League watches in amusement. Either Dr. Horrible leaves the League in disgust, muttering about falling standards, or he gets his eye-twitch again and shoots Hammer with his latest disintegrator gun.

Wonderflonium is
That's right! It can't be bounced. Why is that? If it is bounced, it goes from its meta state that is a power source to its original state upon the next use. The bounce destabilizes the molecular bond of the Wonderflonium in such a way that the next electrical pulse triggers its explosive return to  If it's not kneaded or pressed against paper, then the return is the safer, more familiar method of return to the original state.

The entire show is a Silver Age style Imaginary story.
It's a bad dream being had by Dr Awesome ("I have a PHD in awesomeness!!!"), a Tom Strong style gadgeteer hero, whose Crimefighting with Cash has not only reduced crime to a minimum, but whose wonderful inventions and push for social reform (aided by his girlfriend and later wife Penny) have created a utopian society despite the constant intervention of his archnemesis, the loutish and fascist Mr Hammer. He wakes up right at the conclusion of "The Nightmare's Real", and promptly goes up from his underground HQ/basement to his mansion, kisses his children Billy and Penny Junior (who are already training to take up the mantle) goodnight, and slips into bed beside his wife Penny.

And they all lived happily ever after.
 * Aw shucks.
 * I'd say Captain Hammer sounds more like a Communist supervillain possibly with a sidekick called Little Sickle.
 * Well, there are the hammer-nazis from Pink Floyd's The Wall. That's actually what his insignia made me think of.

Half the story is Billy's delusions due to his concussion.
Take a look at the coloring of the scene where he explains "I need to watch what I say on this blog." It matches the coloring of that final shot of Billy in normal clothes, although the camera angle is somewhat tilted. Tilted and fuzzy, which increases the chance that he's begun hallucinating. After Captain Hammer threw a car at Billy's head (witness the bruise - Billy must be a little hardier than he seems, or else the car only grazed him), Billy managed to make it home, only to lapse into severe hallucinations due to his concussion. This came directly after the phone call from Bad Horse, and so the need to kill or be killed is what drives the rest of his vision. ...not so sure on what caused the costume switch, but possibly he was already somewhat hazy when he got back and only imagined that he had his costume on.

Captain Hammer will return with a cape.
It doubles as a security blanket.
 * This is now canon in my mind.
 * As an addendum, his clothing may be all black (with some white), and he will be GRIMMER and DARKER. Like Frank Castle.

One of Bad Horse's superpowers is teleporting ghost cowboy assassins
It's the only way those Bad Horse couriers work and one of the reasons Bad Horse is so feared: he can have a three-man squad of singing ghost cowboys (they have to be ghosts because you can't see the lower halves of their bodies) teleport wherever he wishes to kill anyone who opposes him.
 * Aren't those the writers? Therefore, Bad Horse's ability to control the writers makes him an extremely powerful foe.
 * Only one of them (Jed Whedon) is a writer. The other two were supposed to be Joss and Zack Whedon, but they couldn't do it for reasons I don't remember, so the other two cowboys are Rob Reinis and Nick Towne, who also play the two moving guys from "So They Say."

The exploding death ray took away Captain Hammer's superpowers.
First off, while explosions aren't fun, odds are that can't be the first blow of that magnitude (or even NEAR that magnitude - he jumps from never having felt any pain to unbearable pain) that a seasoned superhero would take. And even if it was just a much harder blow than his super-strength could keep him totally protected from, he is still in crippling pain days later when he talks to the therapist. That doesn't sound like one painful blow. That sounds like the removal of his inability to be hurt. Since he has not had a lifetime to get used to everyday bumps and bruises, this new sensation is too much for him to bear. It also explains why he hasn't even tried to get back on his feet and has hidden from the media; he can't continue being Captain Hammer.

Either that, or it severely injured him, probably internally since we can't see it. The pain is now omnipresent and, again, is something he's never had before even in small doses. He's in no shape for heroics and in perfect shape for someone to come finish the job if he doesn't drop off the radar.
 * "Blow of that magnitude"? It's a death ray. The explosion is more than heat and kinetics. It's an explosion of death.
 * Though it seems more likely that Captain Hammer is a complete baby when it matters. He isn't constantly in crippling pain so much as traumatized by his one exposure to it. If he did lose his powers, though, he would have a more legitimate reason to be going to a therapist. Can anyone actually make out what he's saying to that guy?
 * Word of God says it's canon that yes, that being the first pain he'd ever felt, even if it was like a paper cut it would be comparatively agonizing.

Dr. Horrible is set in the Firefly universe.
In "Brand New Day", when Horrible sings about giving Penny "the keys to a shiny new Australia", he means "shiny" as in the slang for cool used in the Firefly 'Verse; the new Australia refers to the fishy planet of New Melbourne. Dr. Horrible destroys the Earth in a rage, and Firefly is set in the future. The same unreliable and interfering authorities who lock up children for showing signs of high intelligence (as seen in the Captain Hammer comic) later decide to start experimenting on them instead. Mal is the descendsnt of Captain Hammer, which explains how he's able to endure the pain he receives.
 * The Death/Stun Ray became the basis for the designs those guards carried in "Ariel".
 * For that to be true, either you'd have to have time machines, or a designer of the Firefly cruisers would have to be a Doctor Horrible fan. If you look in the background as the good doctor does his blog, you can clearly see what appears to be Serenity.
 * Jossed, apparently that's just "a collection of pots and pans hanging in a window in Dr. Horrible's lab".

Bad Horse is the horse once made a senator by Caligula.
He became so accustomed to power that he became an immortal supervillain.
 * I don't know who you are, but that's brilliant.
 * This is the single best WMG this Troper has ever had the privilege to read. I thank you, good sir, for the honor of experiencing it.

Dr. Horrible, The Tick (animation), and The Venture Brothers all take place in the same universe.
First, take a look at this interview with Joss, which places The Tick and Dr. Horrible in the same universe via Word of God. Getting from there to The Venture Brothers is a bit of a stretch, but Ben Edlund (creator of The Tick) has written for the show, and in one episode a passing reference to a minor Tick villain, Pigleg, is made. Naturally, this would also place all of these shows in the Jonny Quest continuity as well. The relationship between David Bowie of the Guild of Calamitous Intent and The Evil League of Evil's Dead Bowie would have to be explored.

Johnny Snow is (or was) Dr. Horrible's biggest fan.
Young, shy Johnny loved Horrible's blog so much, he wanted to become his sidekick. But when he was heartbroken to discover that position taken up by a sweaty guy, Johnny became a superhero in a desperate attempt to try and get Horrible's attention. In a way, he's the anti-Syndrome.
 * Alternately, he never stopped admiring him. Since approaching the guy and asking to be his sidekick just isn't the way these things work, Snow wants desperately to get the chance to fight Horrible so he can invoke Defeat Means Friendship.
 * Alternately, Johnny Snow is one of Dr. Horrible's own little group of fans, and in denial of his man-crush.
 * Alternately, Johnny Snow is a villain - no one said that villains can't have other villains as nemeses. "Slipping" implies that Captain Hammer's the only hero around. (maybe the fee's too pricey/for them to realise/your disguise is slipping) This basically makes Snow the Syndrome.

Billy is Doogie Howser.
Alienation due to his unnatural intelligence as well as the frustration at being called Doogie led him to change his name and undertake a life of crime. Come on, people, it's obvious!
 * My god, this makes so much sense!
 * It seriously does. The entries Doogie makes into his journal at the end of every episode -- remind you of a certain villain's blog? And anyone who's seen Doogie express his views on the state of the social system and homelessness and the like can easily see the parallels. For example, in the episode "Every Dog Has His Doogie," Doogie is perfectly willing to break the rules or his friends' and family's expectations of him to achieve what he thinks is morality. This happens a lot. His poster in his bedroom, "Save the Humans"-- sound familiar? It also brings up the possibility, or probability, that Horrible's doctorate is not morally ambiguous at all, which can be evidenced by the gizmos around Horrible's lab (brain scans, models of the digestive tract, etc.)! Also, both Doogie and Horrible live(d) in the same city -- Los Angeles!
 * Watch "Doogenstein" and tell me that is NOT a young Dr. Horrible.

Bad Horse is the main character.
He orchestrated everything through his agents Penny and Captain Hammer (see above). The goal was to turn Dr. Horrible's super-intelligent brain to the side of evil.

The story is an allegory for anti-intellectualism, especially in politics
The only things that we see as the world being mad are Captain Hammer being accepted (by people and Penny), and Dr. Horrible and other intelligent people being rejected (by people and Penny). It's similar to how in many facets of life, especialy American politics, charisma is valued over intelligence, and intelligence is often seen as a negative trait. But the intelligent respond to this by being self-righteous, socially awkward, know-it-alls, etc., which only makes the problem worse. Campaign rhetoric, when interpreted logically. When you choose people solely based on charisma, you get flaws similar to Captain Hammer (philandering, taking credit for everything).

Billy/Dr. Horrible is a reincarnation of Alexiel from Angel Sanctuary.
Even before the whole love-triangle with Penny and Captain Hammer, he still had a pretty crappy life: Getting beaten up by a smarmy jackass is humiliating, and he gets severe injuries at least part of the time (dislocated joints essentially cripple the limb until you get to a doctor--you can't just shove it back in, or else you'll mess up your nerves). His compassion for others (refusing to fight near a park because children play there, and refusing to kill a young future President or his mother) may be a residual trait of Alexiel's, which was purposefully brought out because, while basic decency is expected for normal people, Billy's compassion specifically conflicts with his hopes to get into the Evil League of Evil--another source of frustration for him.

Once he starts to get resigned to his Designated Villain status, he is no longer (as) tormented; YHWH makes sure that he's still miserable by setting up Penny and Captain Hammer. Hammer being aware that he's dating Billy's dream girl was the icing on the cake. Penny herself may be a reincarnation of Jibril, who "protects" Billy in this life by helping him keep his morality and compassion; but her protection is slowly eroded due to Alexiel's required misery and YHWH's manipulation, and Penny's last attempts to help Billy fail because of her death. After that, YHWH's job is done because Billy killed an innocent person and the love of his life without ever telling her how he felt. His acceptance into the ELE will always remind him of that, and he will spend the rest of his life suffering because Penny isn't there to help him through it--and it's his fault.

Billy's a Cosmic Plaything to the max.

The entire cast is C-List Fodder
The newspapers reporting "Country Mourns" and "Worst Villain Ever" is hyperbole used by overzealous reporters and journalists. Captain Hammer is an incompetent Superhero who only works in a single city. Billy desperately tries to be taken seriously, but there's nothing he can do to compare to the likes of Lex Luthor, Zoom or Sinestro. The Evil League of Evil is the local crime syndicate who stay local because they know that the moment they get the attention of an A-List superhero, they'll be knocked down faster than a house of cards.

The Blog is a huge analogy for the Writer's Strike
Think of it--a poor, sympathetic protagonist sacrifices everything, including his principles, to join a prestigious league, while crazed fans just chomp down on whatever fodder comes their way, and jerks called "heroes" run the entire system? And to take a leap of faith, would that make Joss Horrible, or... Bad Horse?
 * Canon, as sung in Commentary! The Musical

It's all a product of Billy Buddy's imagination (save the last 2 words)
He's just a lonely, possibly clinically insane, man with nothing but an overactive imagination.

Bad Horse is Suzumiya Haruhi
Pretty much the only major fantasy Haruhi hasn't lived out yet is being a supervillain, and Bad Horse's heraldic cowboys look suspiciously familiar.
 * Also, becoming a horse might appeal to something from her childhood. When a young girl in a cartoon wants something unreasonable, often it's a pony.

Billy is The Master of Doctor Who fame
Toward the end of the Doctor Who episode, Utopia, the Master is, his personality sealed away as a method of keeping him imprisoned. Possibly, Billy is in the same situation, a future incarnation of The Master thrown to some far-flung corner of space and time with the "evil" personality sealed away, leaving a well-meaning but rather wet young man with an amazing mind.

However, as life takes its toll on Billy and he suffers humilation and defeat, the mental blocks break down; the older personality reasserts itself, leading to a progressively more dominant "Doctor Horrible" (possibly a reference to his old foe, and his thoughts on him?) taking complete control, with the cover personality removed. Give it a few more weeks and Doctor Horrible will be dancing to I Can't Decide as he torments Captain Hammer.

Billy read Twilight
Think about it: he thinks that stalking a girl and generally being evil is the way to win her heart. If you get your love advice from Twilight, that kind of impression is to be expected. Even if you like Twilight, you can't disprove this theory because, even if he liked the book and considered Edward a role model, he would still try to mirror his actions.

Captain Hammer became a good guy
After falling in love, he means what he says about everyone being a hero and only threatens Dr. Horrible after fearing for Penny's life. The therapy is for his subsequent mental breakdown. He'll try to kill Horrible next time when he realizes how dangerous Billy is.
 * Except that what he says about everyone being a hero is incredibly arrogant, setting himself up as always a better hero.
 * Baby Steps.
 * Buzz Lightyear's also arrogant except Captain Hammer's an idiot and doesn't know that asserting his own superority for half the speach is a bad idea. What makes Captain Hammer seem evil and not just stupid is the fact he basically said I'm going to sleep with her just because I can and you can't to Dr. Horrible. If you want you can say he was trying to make sure Dr. Horrible wouldn't hurt his love.

The series is a Blog Suicide Letter
The parts where the doctor is talking to the camera are pieces from his blog, the fantasy sequences were taken from his mind by some machine he invented and the events happening in reality were taken by nanite-cameras he built to document his joining of the Evil League of Evil. Moments after making his final entry he kills himself.
 * The Evil League of Evil is in or in charge of hell, hence supposedly-Fake Thomas Jefferson and Dead Bowie and everyone looking like a Tim Burton villain reject. The Evil Costume Change isn't because he's dead, it's just one of hell's dress code! "There will be blood, it might be yours, so go kill someone, signed Bad Horse"... It's not If You're So Evil Eat This Kitten, the only way to get there is by dying!

There is a Neutral League of Neutral in charge of both the supers and villains.
The Evil League of Evil isn't as Evil as it could be, especially considering Captain Hammer seemed to be the only superhero that mattered to the press, and completely disappeared after the Death Ray incident. Captain Hammer doesn't look like the kind of guy who would stay a superhero instead of using his abilities for Mundane Utility (at least becoming a movie star), or even becoming a villain, so there's probably someone in charge to make sure the heroes don't get bored and the villains don't get away with any unacceptable casualties.

The car did hit Billy directly in the head.
He went limp when he saw the car flying at him, and the car merely pushed him under it. He likely had more pain in his neck than his head, even if it only grazed him. Possibly, the goggles saved him by absorbing the excess kinetic (but somehow not heat) energy, similar to the freeze ray, so it was more like a mylar ballon hitting him at 30mph than a car.
 * He said Captain Hammer threw the car at his head, but he never said the car actually made any contact. All he's saying is that the car came in his direction.

Brand New Day with Giant Doctor Horrible was a flashback, not a daydream.
He can survive having cars successfully thrown at his head due to an inversion of the Square-Cube Law's use in most media.

Members entering the Evil League if Evil must kill their loved one to enter the Evil League Of Evil, and resurrect and turn them to advance in the ranks.
This sith-like "subjugation of nature" attitude explains Dead Bowie (By Tie Die?) and supposedly-Fake Thomas Jefferson (probably brought back by an unseen and possibly permadead former member). Penny may be the future Fro-Yo, or Nurse Horrible, assisting the doctor with his freeze ray.

The entire show was created for the sole purpose of making Neil Patrick Harris the definition of cool and encouraging people to emulate him.
In "Everything You Ever", Dr. Horrible sings, "Now Dr. Horrible is here / To make you quake with fear / To make the whole world kneel". However, once you remember that Horrible is played by Neil Patrick Harris, you can also interpret that last line to be, Hey, it's called Wild Mass Guessing for a reason. Also, people have thought of stranger plans.
 * This Troper had a very similar idea, and in fact came to this page just to pose it. To wit:
 * This troper's extrapolated the above theory:
 * Possibly dovetailing this with the "Dr. Horrible is the Master" theory above, bearing in mind

Doctor Horrible will use How I Met Your Mother's Barney as his civilian persona.
Both characters begin as well-intentioned but timid, have something go very wrong with a girl, and in response seal up their hearts and become soulless bastards... though Barney's is played for laughs. Admit it: it's creepily possible.
 * That's been a part of this Troper's personal canon since he started watching How I Met Your Mother.
 * It's been a part of this Troper's canon, too, ever since reading the magnificent fanfic Billy Stinson.

Captain Hammer was physiologically scarred by a homeless person when he was a child.
The way he flinches from the homeless, describing them as "a bunch of scary, alcoholic bums"...
 * Do you mean psychologically? There's a huge difference...

Captain Hammer never had any superpowers
The online comic is from his perspective, and notably over-the-top, so him throwing Dr. Horrible that far could easily be an exaggeration. His ability to avoid pain and defeat villains could be attributed to his ability to get the first punch consistently, and we never actually see him "throw a car" at Dr. Horrible, so that could be an exaggeration too. For all we know, he's just a very strong braggart who's never experienced real pain before.
 * Apart from there being no real reason not to take Dr. Horrible at his word, Captain Hammer surviving the exploding death ray at point blank at all, the sheer distance he got tossing Penny to one side, and his general reputation as a full-fledged superhero, it says a lot that he was fully prepared to stop an out-of-control van with his bare (well, gloved) hands. Turned out not to be necessary since Dr. Horrible managed to get the brakes working, but he was clearly banking on super-strength and invulnerability at that moment.
 * There's also a brief scene during his date with Penny where he pedals a two-person pedal-boat around comically fast. I do like the way you think, though.
 * It's worth pointing out that Captain Hammer: Be Like Me! was indeed exaggerating his Horrible-throwing-ability. We see the same event in Moist: Humidity Rising, and according to Moist, Hammer just punched Horrible to the ground.

Penny is actually Vi
She was on a mission to redeem Dr. Horrible, possibly as part of a larger plan to get at the Evil League of Evil. Her dating Captain Hammer was meant to communicate to Billy that she likes good guys. The idea was to inspire Billy to outdo Captain Hammer at being a good guy (not that difficult, honestly). They also had an insurance plan in case Captain Hammer went evil after Penny left him for Billy - Dr. Horrible and a Slayer would easily defeat Captain Hammer. "Penny: Thank you Hammer man, I don't think I can/Explain how important it was that you stopped the van/I would be splattered, I'd be crushed into debris/Thank you sir for saving me"
 * This also increases the chance that Penny has survived the ending due to Slayer toughness. Once she recovers, Buffy will order her to kill Dr. Horrible.
 * This would explain her babbling at Hammer after being rescued. Her Slayer powers would have meant she'd be able to easily survive being hit by a van (Buffy herself was hit by a truck once and got up with barely a scratch on her). When Penny was saying thank you she wasn't in shock, she was overcompensating.

Penny is actually Cyd Sherman
While we're randomly guessing that every role played by Felicia Day is the same person (see above), let's add that Penny is actually Cyd Sherman. After the events of Doctor Horribles Sing Along Blog, Penny got raised using a magic spell from the RPG the Guild play. As a result of having magic from the game cast upon her, Penny became incredibly addicted to the game. She tossed away her old life and name, and started playing the game 24/7. Speaking of games, you just HA! (That's just how I laugh.)

Cyd Sherman is actually Penny.
At some point after the events of The Guild, possibly after a Downer Ending- which would explain her references to a really terrible love life- Cyd quit the Game and changed apartments. Getting more than three hours of sleep per night (on a regular basis, no less!) made her considerably less neurotic and more optimistic. She needed something to do with her time, so she started volunteering at a local homeless shelter.

The Newswoman is an Active.
Captain Hammer hired her to say nothing but positive things about him to boost his PR. He's certainly got the clout. And in the song "So They Say," she has the line "Let's all be our best." Eerily similar to "I try to be my best."

Captain Hammer really is just a good guy.
And Dr. Horrible is just deranged. The only evidence we see for the world needing social change is that everyone likes Captain Hammer. Sure, he's a bit of a git sometimes, but he's a legitimately good guy, he even tries to help the homeless, it's unlikely that he's just helping them for Penny as he already has a fanclub of people willing to "do the weird stuff" with him, and he was interested in her before he found out that Horrible was. The only bad things he does are being mean to Dr. Horrible (a supervillain and criminal who logically should be in jail), brushing off his shoulder after that guy touches him (So he likes being clean), and his song "Everyone's A Hero," which to me seems more like he's failing at public speaking than someone whose obsessed with himself.
 * While I admit that "Everybody's a Hero" sounds more like someone who sucks at public speaking, it is also extreamly self obsessing. Really, everyone is completely apathetic except Penny, although I wouldn't say that Billy/Dr. Horrible cares about that.
 * Hammer lets the runaway van nearly careen into Penny because he's busy singing about how great he is. In the comic he encourages reporting smart and weird kids to the cops as potential supervillains. As for the homeless shelter business, it might still have been to get with Penny, because he directly states he's just dating her to piss off Horrible. Besides, one of the moving guys notes that the shelter is the only time he's used his fame to help people ("about time").
 * He was also arguably prepared to murder Dr. Horrible in cold blood after "saving" Penny, and undoubtedly either trying to publically execute him or somehow humiliate him by revealing that the ray doesn't work (remember, he was frozen and didn't see it in operation).

The Evil League of Evil is a cover for The Pride.
Captain Hammer is really one of their agents disposing of superpowered compition under the guise of a hero. It is because he got accepted into the leauge that Hammer stopped picking on Billy not because he was defeated. Besides LA isn't really a hot spot for super activities in most universes and they both had Joss Whedon writing about them for a while.

Wonderflonium is used to focus ray devices.
Think about it. Before Dr. Horrible got the Wonderflonium, the only ray he had that worked at all was the transmatter ray. It snatched up soup instead of gold bars because it wasn't sufficiently focused to get into the vault, and hit someone's lunch instead. The muscle-ray just clicked, and didn't work at all. It's outright stated that the freeze ray requires wonderflonium. Finally, "Do Not Bounce". Clearly, the death ray used wonderflonium, because it exploded immediately after bouncing.

The car missed.
Captain Hammer through a car at Dr. Horrible's head. He missed. The end. No hallucinations. No exagerrations. He just missed.
 * That seems to be the general consensus, especially considering that Dr. Horrible still has a head.
 * Because, for whatever reason, the standard laws of comic book combat are assumed not to apply in this world. Go figure.
 * It's a Deconstruction. Of course the combat is more realistic.

Dr. Horrible is a younger version of Nathan from Repo!The Genetic Opera.
...just imagine how screwed-up that would leave a guy...

Wonderflonium is an isotope of narrativium.
Specifically, wonderflonium is the common term for narrativium-14 - although it has differing physical properties, it retains the most basic feature of all elements in the narrativium family (other elements include alliterium and tropium) - narrativium-14, wonderflonium, behaves in certain ways simply because the plot says so. Examples: In Act I, Captain Hammer completely destroyed the Horribe Van Remote receiver. It only started working again because the wonderflonium inside the van generated a field of... plotness, and the plot said that the remote worked again just in time. In Act II, the freeze ray fails, because it runs on wonderflonium. The plot states that Horrible's heist in Act II must fail, or Act III would never have happened, so the wonderflonium's failure following the plot. In Act III, the freeze ray fails again. Not only that, but it fails at exactly the perfect dramatic moment in terms of plot. How can this be? Because the plot says that it does, and narrativium-14 follows the plot.
 * That's also why the Death Ray exploded and killed Penny. The plot said that it was supposed to work and Captain Hammer killed Dr. Horrible, which would become Penny's own Start of Darkness, but the Wonderflonium in the gun had been bounced, so it screwed up the plot.

The entire show is from the perspective of Dr. Horrible narrating the event in his blog.
This is why Billy's painted as the victim, Hammer is such a blatant jerk/idiot, the townspeople don't catch on, and Penny's idealized to the point of being a flat character.
 * Is this a WMG? It's just about as close to canon as a conjoined twin.

Act III, from the shelter onwards, was from the perspective of the Reportress.
Yes, the Reportress (of Terror Island fame), disguised as a normal reporter. The one who wrote "Horible", specifically. Her superpowers are: mis-spelling "horrible" without assistance, and Mad Reportin Skillz™.
 * With her Mad Reportin Skillz™, the Reportress could tell that Captain Hammer was a total jerk. He didn't actually sing "Everyone's a Hero", despite being a huge jerk - he sung an actual inspirational song, and the Reportress "embellished" the lyrics with her knowledge of his character.
 * When Doctor Horrible arrives, the Reportress uses her Mad Reportin Skillz™ to discover his actual motives (ELE, Penny, etc.). Because "Slipping" is incredibly awesome, the Reportress simply recorded the lyrics as they were, no embellishment necessary. When she's mis-spelled "horible" (sic) on her journalling paper, she's not writing about Doctor Horrible. She's actually written: "Anarchy! That I run!/It's Doctor Horible's turn!" (sic), and when Doctor Horrible spots this, he helps her correct it.
 * Finally, the Reportress fled the scene when the death ray exploded - she did see the shrapnel's destination, however, and wrote "Everything You Ever" based on the evidence of the shrapnel, and the knowledge of Horrible through Mad Reportin Skillz™. She wrote the tune based on Mad Reportin Skillz™, and most of the lyrics based simply on supervillain cliche statements.
 * After all this work, the Reportress found Neil Patrick Harris, Nathan Fillion, and Felicia Day. She got them to do a re-enactment of the shelter scene, based on what she'd written down. This is what we see in Act III. What really happened in the shelter? We may only learn in the sequel.

The entire Blog was created to advertise for The Guild.
If Penny wasn't killed, she couldn't have "shilled for The Guild" in Commentary!. Therefore, the entire plot of Doctor Horribles Sing Along Blog is merely a front to allow Felicia Day to insert advertising into something by Joss Whedon - since anything by Joss Whedon is watched by nerds, they're exactly the target market for The Guild as well!

Billy's full name is Billy Horrible.
And he has a PhD in Applied Quantum Physics, not in Horribleness. Captain Hammer was made a captain when he signed up for the military's Super-Hero Home-Front Initiative, like state alchemists and possibly EVA pilots automatically get an officer rank.

The entirety of Act 3 was an imagination spot...
Where Billy was trying to prove to himself that he didn't need to feel, and failed. That's what the last part of the final line was- getting choked up at even just imagining it, and knowing he couldn't

The Death Ray works by making people into plasticine.
Not literally. Captain Hammer became vunerable because of this, and Penny was killed because the shrapnel was still charged with the plasticination-power. If Captain Hammer's powers work in a way similar to the AT Field of Neon Genesis Evangelion, it could easily be that his field is strong enough that is can't be dented with knives or bullets and disrupt his physical body]], which seems quite likely considering it hurt in his heart. This could be backed up by "it's gonna be bloody" in the song. If it worked like a typical (for a non-explosive) death ray, it would most likely have simply killed him to death instead of anything bloody. It could have been that Doctor Horrible didn't know if it was going to just make Hammer really weak and vulnerable to the point he couldn't stay alive, or if it would completely destabilize him (though, Evangelion Spoiler: ).
 * Killed him to death? How many other degrees of killing do your Death Rays let you reach?

The Death Ray had no wonderflonium.
It didn't bounce, it just cracked. The energy hit Captain Hammer through the cracks and made him vulnerable to shrapnel.

In the final scene, Doctor Horrible's new gloves are the same as Captain Hammer's.
Probably just from the same Super Costumes Outlet, but they could be a trophy. And we don't see Captain Hammer after the scene at the psychiatrist's office, so they don't have to be another pair.
 * Yes they do. Captain Hammer's gloves had ridges along the back of the hand. Horrible's were pure rubber. Also, it's possible that Captain Hammer cannot remove his gloves, be they fused to or the actual skin of his hands. Or perhaps his hands are some horrific amalgamation of steel and flesh. Wildly mass guess about it.

Captain Hammer wears gloves to keep from breaking the skin of his knuckles.
Only his skeleton is invincible, and his muscles became unusually-but-not-necessarily-super-strong to compensate. He has an inability to feel pain, so he just makes sure to rely on his boots and gloves to keep his bones from ripping through his skin when he punches a villain too hard. The death ray jump-started his nervous system instead of shutting it down.

TheWarehouse webcomic is the future of Doctor Horrible.
Ball, Peen, and Super Dick were separated from Captain Hammer. Hammer acts just like Super Dick would with a bit more motivation. What caused this lack of motivation? Ball and Peen being separated into their own characters. If you recall, the hammer is his penis, and Captain Hammer's motivations appear to be primarily getting sex. Doctor Horrible became Charles the Raver after he tried to kill himself, but took psychotropic drugs instead of sleeping pills and decided he liked the feeling enough that life was worth living and the world was worth saving (his full name is William Charles Horrible). The various themed characters would seem to fit perfectly with the supers theme in Doctor Horrible (that is, puns and uselessness), as would the villains (numerous and ineffectual).

Doctor Horrible is the good side and Billy is the evil side.
He always shows the most remorse and is much less manipulative as Doctor Horrible. He sings Brand New Day as Billy, and the closest thing Doctor Horrible gets to a Villain Song is Slipping, which could be about his roles slipping (like WMG has assumed), but in the other direction. Billy wants to be a super villain, and stalks Penny and puts on a false front to make her like him, but Doctor Horrible only once makes anything stronger than a stun ray and shows what appears to be genuine emotion the one time he interacts with Penny.

The Hammer is his yacht.
Captain Hammer's "the Hammer" is his penis the same way a knight's lance is his penis, or Lord Faarquad's castle was his height. That's why he's Captain Hammer. And it answers Penny's question of what he's captain of.

The Guy Who Smells Like Poo is a spy for the Evil league of Evil.
He was standing by the fire drum behind Billy at the same time that he was in the homeless shelter having soup. There are at least two of him, probably psychically linked and possibly a Multiple man. The smell that smells like poo may be a side effect of his power, or it could be method acting.

Doctor Horribles Sing Along Blog is a Show Within a Show.
Specifically, it's within Commentary! The Musical. Simple.

Everything after Brand New Day was a what-if scenario.
(Yes, it's another one of these.) Billy headed back to his apartment/lab, intent on bringing about Hammer's demise, but something made him reconsider. Maybe Moist talked him down, or maybe he just needed some time to cool off. He decided that it was too risky, and the likelihood that someone innocent would be harmed was too high. But he didn't want to abandon the idea completely, especially since the ELE would  if he did. So he and Moist paid a visit to Hourglass, whose conveniently only-vaguely-alluded-to powers include not only seeing into the future, but living it or allowing others to. Hourglass put Billy into a trance, and in his mind he went through with his plan - of course completely unaware at the time that it was a what-if. (This could also explain why time seems to pass so quickly in the last part of Act III.)

Shortly after the last shot, Moist and Hourglass manage to snap Billy out of it. He is horrified, and, naturally, decides not to go through with it.

Dr. Horrible and Johnathon Coulton's song "Skullcrusher Mountain" describe parallel universes.
It's just that in Dr. Horrible, he met Penny before he completed his rise to supervillainy, mostly because Joss is an evil, evil person.

"Johnny Snow" is, in fact, a woman.
With the name Joni Snow.
 * This troper would like to ascribe to this theory as well, and propose an alternate form. Johnny Snow is a woman (or an androgyne) who thinks she'll get by better in the whole superhero-supervillain thing with a male persona.

"Johnny Snow" is, in fact, Penny.
Obviously this requires the previous WMG to work. In order of events:
 * Penny becomes Johnny (Joni?) Snow.
 * Either she repeatedly arranged "battles" with Horrible to reveal her true persona to him, but never getting the chance due to his constantly spurning her for Captain Hammer; or she adopted the Penny persona after being rejected, in order to secretly get back at Horrible.
 * Since she clearly watches the vlog, she knew what day the Wonderflonium heist was. She deliberately came up to Horrible when she knew the courier van was about to be loaded, in order to make him feel guilty; she intended to finish this off by deliberately stepping in front of the van, faking her own death with an impact-absorbing undershirt.
 * Captain Hammer put a stop to that plan, but Penny realized she could drive the knife even deeper by going out with him. Eventually, she got too fed up with the buffoon to go on any further. When the Death Ray exploded, the undershirt protected her from the shrapnel, at which point she faked her own death as she'd originally planned.
 * And Penny loves frozen yogurt

Captain Hammer really was falling in love with Penny
He's never been in love with someone (besides himself) before so he's not used to it. If she had lived then she would have dumped him and he may have realised that he's a jerk and actully attempted to improve himself.

The sequel will be "Penny's Sing Along Blog"
We will see the story from her point of veiw, including what made her think that Captain Hammer wasn't a complete jerk among other things. This will also explain her final comment.

or the sequel will be Captain Hammer's Sing Along Blog
Same as above except with Hammer.

Penny is the true hero in this show
I know it's a little sappy, but think about it. She's not perfect like Billy wants to believe, but she is the true hero. She is the only selfless person who desires is to be a symbol hope for others. Her death repesents the end of true heroes as everyone just shifts over from apathetic hope to apathetic fear. Penny repesented true change for the better.
 * I think this might be right. Everyone in their world seems to treat the battle between heroes and villains (and resulting damage) as pure entertainment. When Captain Hammer supposedly becomes "a crusader", it's treated like any celebrity advocacy -- something to be fawned over more than anything. And when Dr. Horrible goes on his rampage in the auditorium, notice just how many reporters stay -- and how no law enforcement shows up. All right, their world clearly sucks, Billy was right. But for all he talks about "social change," he's clearly playing the game as much as the next guy -- he's trying to get famous, and get all the perks that come with that. On top of that, he stalks Penny and treats her as a prize to be won back from Captain Hammer. Penny, meanwhile, is the only one genuinely trying to help anyone, and just make her way in the world. Her death, not Dr. Horrible's reaction to it, is the real tragedy of the story.

Penny would have dumped Hammer if not for....
... the fact that he help her get the building she needed for the homeless, and she would have felt terrible and others would have assumed she slept with him to get what she wanted.
 * For that matter...

Penny slept with Hammer to get what she wanted
All for the sake of the homeless. I can't bring myself to hate her....
 * Though Hammer's fangirls can, possibly feeling this way after comparing their personalities.

"Johnny Snow" is Jon Snow from A Song of Ice and Fire
Which makes the entiredy of Dr. Horrible's Sing-Along Blog actually a commentary on the wars in Westros. Penny as Sansa Stark? Moist as Tyrion?

In the sequel Dr. Horrible and Captain Hammer will go at each other.
Ok, I know this one sounds obvious, and most people seem to be expecting Joss to do something unexpected, but I think going the obvious route would actually be appropriate in this case, given some of the above theories. After all, now that Penny's dead, the real Dr. Horrible is awake, and he won't be holding back. Furthermore, for the first time in his life Captain Hammer had been beaten, and so for the first time he'll actually be recognizing another person as a threat to him. So, I think the results will actually be the two being absolutely ruthless for 40 minutes.

The ELE uses a blood-in blood-out system.
For those unfamiliar with this, its a system common in prison gangs, where you must commit a murder to get in, and are killed if you leave. It helps to filter out cops, who wouldn't kill for admission. It seems that the Evil League does the same, at least to an extent. Apparently they were willing to let Dr. Horrible in if he committed sufficient crimes without killing at the very beginning, which presumably would have still required him to wreak more havoc than a cop would be willing to, but it explains why they decided a single murder was enough to get into a major supervillain organization.

Captain Hammer is Superboy Prime.
That's why he has sweater vests - he's trying to be like Superman. It also explains why he's such a dick.

Billy and Dr. Horrible are the same person. Gasp!
Just throwing it out there. Dr. Horrible and Billy, are in fact, a single coherent mind, not a split personality. This would explain why he has exactly the same mannerisms and shows the same goals and emotions, except for being slightly less shy as Dr. Horrible (which is to be expected, since he's using a costume and alter ego), and even then it's only because until the end he has no direct interaction with Penny in costume to MAKE him go Shrinking Violet. It would also explain why he's just as likely to act evil while dressed as Billy (starting Brand New Day) and can cry remorsefully as Dr. Horrible (Everything You Ever). Really, it should be a given that there is no split personality, merely a single character who experiences a tragedy brought about by his own myopia, but because of the prevalence of the Fanon, I'll just lump this in as another theory.
 * Some people also feel empowered by wearing the costume. His so called evilness is him being confident. It's not a split personality, it's a sad story. Just like in Watchmen with Dan and Nite Owl. He's only confident as Nite Owl, but Nite Owl is essentially Dan Dreiberg.
 * Yes, this is what I was getting at. He's not as shy as Dr. Horrible because he is empowered in costume and because there are few Penny scenes to make him crumple. Almost everyone experiences it in some form. Taking on another persona who is meant to be greater than you and is made to appear "separate" from you is of course going to be psychologically liberating in many ways.
 * Like Marvel's Sentry, or JLU's Hawkman/Shadow Thief, they could be two products of the same Freak Lab Accident.
 * Thank you for mentioning this. I've always looked at it this way, and seeing 'Dr. Horrible' and 'Billy' constantly referred to as seperate people was really odd to me. I was planning to add this if no one else did, and you put it much better than I would have.

Dr. Horrible has a superpower, and it's simply being Made of Iron.
I have some evidence to support this one. When he's hit by a car, all he has are a few bruises. When the Death Ray explodes, killing a person and injuring Captain Hammer, he's completely uninjured. Hammer also beats him up by slamming his head on a truck repeatedly, as well as what's shown on A Brand New Day, as well as a punch right after Slipping. This makes perfect sense, (more than 99% of the things on this page) and explains what was formerly just a way for Joss Whedon to indulge in his trademark girl murder. And that's not even talking about his personal life.
 * This actually does make perfect sense, as surprised as I am to say it. Many people just Hand Wave the "threw a car at my head" thing as Captain Hammer threw a car and missed, and Billy was just pointing out how extreme that was. On the other hand, he has a gigantic bruise over his face, showing his face and head were hurt. This was usually taken as Captain Hammer beat him up afterwards. But the line is funnier and simpler if you interpret the bruises as the car actually hit him. In which case he would need such powers to even have a head still on his shoulders. It would also explain how a guy who can pick up and throw a car could punch Billy and show intent to kill in Act III, and send Billy across the room, without leaving so much as a scratch. Or we could just chalk it up to the MST3K Mantra in a comic-book style world allowing a non-powered Billy to take the abuse.
 * Also, it makes sense that if he only has the defensive part (not being hurtable) and not the strength that usually goes with it, he'd take up science. Think about it, what is one of most common ways to gain powers, if not THE? Accident in the lab. What is the reason you don't experiment with weird combinations of components without a long and tedious process of finding out if there is any chance it'd explode or electrify you? You'd die. So, someone, especially a main character, who works in a lab in a world where powers exist is likely to obtain a power. And someone who can make progress in technology much faster than other scientists is likely to cut some corners. Not to mention, he doesn't have to fear anything other than imprisonment, so a few simple, concealable, devices to escape prison, and he's free to be a major villan without fearing that the heroes will ever manage to hurt him. Notice how his attitude towards Hammer isn't "Oh no! A Hero! My life is in danger!", but rather "Oh great, the idiot's here again"
 * This might also, assuming the events actually do happen outside of his imagination, explain why Hammer doesn't just take him in to the proper authorities. Leaving a few villains out there who can't be stopped by normal cops might be a good business investment for the the town's hero.
 * It's also been said before.
 * He's a scientist he obviously uses science to come up with ways to make himself able to survive such attacks and to heal himself afterwards makes me wonder why he didn't give himself superstrength.

Captain Hammer becomes a true hero in the sequel
The guilt and physical pain from the shelter incident, coupled with the therapy, make Hammer feel empathy for others for the first time. The sobbing he was doing in therapy during the ending montage happenned when he realized what a bastard he was. He becomes a humbler, more compassionate hero (but still an idiot), parallelling Horrible's descent into true villainry.
 * The sequel will be about his fight with Dr. Horrible, who he can never defeat because of guilt over what Horrible became. Hammer may find a new Love Interest, which Horrible will kill in revenge, causing Hammer to kill Horrible, and give up the concept of being a "hero".
 * Or not.

Moist is gay
Well, I'm only basing it on one tiny bit, but, it's the room with the whole girly motif and the guy in pink latex right next to him. But, then again, now he has a use for his powers of making things moist... and slippery... lubricated.
 * So why is he friends with the Pink Pummeler, eh? (Whose room I'm assuming it was, by the way, since Moist is shown in the comics to live in an undecorated one-room apartment, including the restroom).
 * Yeah, because straight people can't possibly be friends with a gay without doing them.
 * Read the Pot Holes, Bury Your Gays is Pummeler's M.O. Whether that sarcasm was trolling or just ignorance... * sigh of exasperation*
 * Am I the only one who got the vibe off the Bait & Switch double-date thing that one of them (probably Switch) was a guy? He doesn't sound disappointed, just a little weirded out.

Moist is bisexual
There's evidence for him being gay, but there's evidence for him being straight too. Near the end of Everything You Ever, when Dr. Horrible goes to the party, Moist is seen flirting with a girl and enjoying it. Backed up, if the above theory about Bait & Switch is correct, as Moist seemed happy with either one of them.

The Transmatter ray didn't transport a gold bullion after all
It transported the person who was guarding it. As people are made up of many more different elements than gold, they simply re-arranged themselves in-transit and turned the poor guard into slop. He also sniffs it as says something suspiciously like 'Smells like human...'
 * It's cumin, as in the spice. It's supposed to be a joke about gold bullion/bouillon.
 * Cumin is a yellow spice, which would look quite a lot like gold. Since we know that Captain Hammer and the police watch Dr. Horrible's blog...
 * "They were transported...in bar form..."
 * If boullion can come in cubes, it can come in bars.

Doctor Horrible is indestructible!
That car that Cap. Hammer threw at him did give him horrendous wounds and/or broke his neck, but he got better.
 * Ditto the Death Ray explosion.
 * Captain Hammer is not indestructible (at least not by that much), and look what happened when he tried to imitate him!

There was a considerable amount of time between the explosion of the death ray and Doctor Horrible coughing.
Given the above theory, Retrometabolism is not an instant deal, and that explosion was a freakin' big one!.
 * Captain Hammer has another type of immunity to death, but that explosion was a little too much... the kind that left him with a closed head-injury type of energy feedback. He probably couldn't feel his legs for a while, and even then, as he said... in his heart, it hurts.

Doctor Horrible's Sing-Along Blog was produced by Doctor Horrible and was a work of fiction in-universe.
And if the broadcast hack during the 2008-2009 Emmy Awards broadcast means anything, he's from (or came to) our universe. Captain Hammer (or Nathan Fillion in costume) is also a villain or henchman, and Penny is aware of the bad Doctor's identity. The main clue that it can't be before the end of the Blog is that Penny knows who it is. The main clue that it can;t be after the Bllog is that. Although it could just mean that.

Doctor Horrible/Billy actually became the Music Meister
Think about it, both characters are voiced by Neil Patrick Harris, both love to sing... hell, The Music Meister's abilities are decidedly non-lethal as well (fitting with most of Horrible's schemes), not to mention a similar taste in main outfits. The only real difference is that the Music Meister claims to have a different background. This alone can be solved by claiming he used his newfound sound powers to brainwash himself into a different persona. The next episode of Batman the Brave And The Bold that features the Music Meister will have to address this.
 * Alternatively, they are Alternate Universe versions of each other, both with the power to induce music on those around them. Billy probably has the same Freudian Excuse about being bullied, but unlike his counterpart, he never discovered the Mind Control singing power--instead his ability just got sublimated into unconsciously making people sing, and he took a scientific path to villainy instead.

Bad Horse is Khartoum from The Godfather
He was reaminted and pure evil as a result. He has a complete disregard for human life after humans killed him for little reason. the cowboys are the stable boys who used to tend to him and have been bent to his evil will. this would also explain hows he's a Thoroughbred horse after all Khartoum was a 600k stud horse...

Dead Not Sleeping (the second e-mailer) is Captain Hammer...
... trying to find out who Dr. Horrible likes, in order to crush his hopes with her.
 * This actually makes quite a lot of sense.
 * Alternatively, Dead Not Sleeping is Hourglass. She's giving Dr. Horrible a warning about him taking any measures to bring  She knows that he would try, and ultimately fail, without that subconscious warning in the back of his head.

Dr. Horrible is the cause of, and product of, a Stable Time Loop
Dr. Horrible enlists the aid of Hourglass to go back in time and rescue Penny before the events of the Sing-Along Blog. However, he overshoots his mark by a couple of decades, ending up before Penny is even born. Frustrated at failing again, he sinks deeper into the Dr. Horrible persona and does what any good supervillain would do -- take over the world. He is eventually overthrown, and a world now fearful of super-science villains begins persecuting anybody who shows even the slightest spark of scientific aptitude. It's into this world that Billy Buddy is born, and after a lifetime of torture in a Crapsack World, he comes to see Dr. Horrible as a misunderstood benevolent dictator, takes up his mantle, and vows to fix the world... and the cycle is complete.

Billy/Dr. Horrible is Lelouch vi Britannia if the timeline hadn't changed.
Both of them are geniuses who want to change the world through revolution, but the Horribleverse follows a more similar timeline to ours, and Dr. Horrible/Billy has a much harder battle to fight because changing the structure of a 300-year-old government is harder than getting a revolution of a people that have been conquered and discriminated against by Britannia. Penny is Suzaku (she also wants to change the world, but through less anarchic means), and Dr. Horrible is probably Clovis.
 * Penny is Euphemia - a still-hopeful idealist who wants to change the world by being kind. The ideological dynamic between Dr. Horrible and Penny seen in "My Eyes" is very close to the dynamic between Lelouch and Euphemia. Suzaku's character type doesn't fit into this story, unless you stretched very, very far and compared him to Captain Hammer, Corporate Tool.

The whole show is a fictionalization of a talented but unpopular high school student's life.
The student (Billy/Dr. Horrible) lives with his equally unpopular brother (Moist) and is trying hard to get accepted to a table of drama geeks who are highly intelligent but very elitist. Penny is pretty much herself and Captain Hammer is an arrogant jock. The freeze ray is actually an act of humiliation and the death ray represents the student's decision to injure the jock as well as humiliate him. When Penny dies, it represents the girl moving away/becoming inaccessible to them both.
 * I agree, with a few additional remarks:
 * Billy Horrible: straight A student. His geekiness coupled with an unfortunate last name makes him withdraw in on himself and study even harder. He decides to use his last name as a Take That and styles himself Doctor because he intends to pursue a doctorate later in life, when he gets out of this crapsack High School. He starts to devise pranks, such as stealing cumin-spiced soup from the cafeteria.
 * Bad Horse: John Horse, a DM. Billy is trying to get in on a Dungeons and Dragons game, but they all ropleplay as Evil (Dead Bowie is Neutral Evil, Fake Thomas Jefferson is Lawful Evil.) He has to prove he can role-play evil, and starts a Blog where he acts like a supervillain. Bad Horse's parents own a western-themed singing-telegraph buisness.
 * Captain Hammer: Matt, Captain of the football team (The Hammers) and known bully. He has a habit of taking Billy's lunch money: notice how he always takes him to the same corner at recess to punch him? Referred in the school as Captain Hammer, or Hammer for short.
 * Penny: the Lunch Lady. She wants the school to build a new Cafeteria, but the board is indifferent. Billy has a crush on her. Hammer offers to drive her home just to make Billy jealous. Things get out of hand. The lunch lady knows what she is doing is wrong because she is much older. She becomes very guilty. Instead of giving the extra frozen yogurts to Hammer she tries to give them to Billy, but Billy stops going to the cafeteria while he is plotting his revenge.
 * Moist: Billy's roommate. Moist doesn't shower often.
 * Billy's rant about the system: school sucks. No one notices when Hammer punches Billy at recess, or cares. Hammer is the idol of the school because he wins football games, so they let everything slide. He suspects Hammer is using amphetamines and cheating, and that the school knows and lets him play anyways, because they have a chance at winning the title. The school board has gone insane.
 * Hammer convinces the Principal to build a new Cafeteria. He doesn't really care about a new cafeteria: the football team has its own dinning room. After all he doesn't want to mingle with the bums (other less-cool students).
 * Hammer * DOES* throw a car at him the day the principal breaks ground on a new cafeteria. It's a Tonka Truck. It smarts.
 * During Hammer's speech at the inauguration of the new Cafeteria, Billy sets his plan in motion. It is a very elaborate pratical joke that involves acid pilfered from the school's chemistry lab. Everyone gets to see Hammer's use of amphetamines had a negative effect on his... hammer. Hammer is utterly humiliated in front of the entire school and runs away crying, shattering his jock image completely. Also, the acid hurts in a way slamming into someone wearing full protective gear and a helmet doesn't: it's the first time he feels that burn. The prank is in so poor taste the lunch lady is disgusted and actually quits, and moves to another town. Billy's ruthless pranks and pratical jokes make him a terror on the schoolyard. He gets accepted at the D&D game, but he realises he's no longer acting, he really is Chaotic Evil.
 * My mind has now been blown. I demand this be made!

Capatain Hammer is an alternate version of Booster Gold.
Their personalities are just way too similar (most of the time).

The whole show is an adaptation of Hamlet.

 * The protagonist is undone by his hesitation to take revenge, destroying basically everything he cared about in the process, despite achieving his goal.
 * Penny is an amalgamation of Ophelia (The Ingenue caught between the men in her life, who dies as a result) and Queen Gertrude (romantically involved with the antagonist, who accidentally kills her in an attempt to off the protagonist).

Dr. Horrible is a grown-up Calvin.
We see numerous instances of Calvin showing tendencies to Evil Overlord-dom, but also of him showing compassion (the baby raccoon) and concern at the state of the world, to the point where he's willing to leave Earth entirely for Mars. When he grew up, he assimilated Hobbes' persona - this also hampered his natural scientific tendencies, because Hobbes was always holding Calvin back from such (never willing to be transmogrified or duplicated, remember). When he grows up, he goes by his middle name instead of his first name (Calvin William Buddy becomes Billy Buddy), but still finds himself beset by thuggish bullies and enamored of quiet, smart girls. He puts his overactive imagination into action by trying to become Dr. Horrible - just the descendant of Spaceman Spiff and Stupendous Man, hampered by grown-up uncertainty and doubt. However, when he snaps, he snaps but good. And finally, what is the color of the lab coat that Dr. Horrible dons in the last scene?
 * Specifically, Dr. Horrible is Calvin, Billy is Hobbes's personality after he has to throw away his stuffed tiger (see Fight Club page), Penny is Suzie, and Captain Hammer is Moe. Even the hair matches up, except for Hobbes of course. Moist is just Moist.
 * Also the presence of the Bad Horse could be a sign that their universe does contain other anthropomorphic animals besides Hobbes.

The wheel fell off
...and hit him in the face.

Doctor Horrible is a grown up Charlie Brown
Charlie Brown is light haired, Horrible has blond hair. Penny is a red-head. Charlie Brown's love is the little redhead girl. Horrible wants to tell Penny he loves her hair.

It’s an AU version of the Harry Potter backstory
A Deadpan Snarker/nerd/antihero and a popular Jerk Jock “hero” are both attracted to an idealistic redhead who believes in The Power of Love. The redhead falls for the Jerk Jock, and the antihero goes over to the dark side. While trying to impress the Big Bad, the antihero inadvertently causes the redhead’s death and is devastated. Sound familiar? Dr. Horrible is Snape, Captain Hammer is James, Penny is Lily, the fangirls are the Marauders, the Evil League of Evil is the Death Eaters, Bad Horse is Voldemort, and Captain Hammer’s therapist is Dumbledore. If the theory is true, the hero in the sequel should be a clone will look just like Captain Hammer but will have Penny’s eyes and her belief in The Power of Love. Dr. Horrible will redeem himself by dying to save the other characters, and Bad Horse will be defeated by The Power of Love.

Dr. Horrible's story takes place in the universe of the League of Extraordinary Gentlemen, wherein every fictional story or character exists and interacts with the others.
This makes sense in the light of many of the above theories (i.e. Bad Horse being a Houyhnhnm, Ozymandias destroying Manhattan, etc.), and allows several alternate explanations for other questions (for example, Captain Hammer may be Kryptonian, a government experiment a la Captain America, a renegade god like Hancock, or a refugee from the Eugenics Wars, and on and on...hey, there's a lot of fiction out there.) It also opens up an entirely new toybox for us fans to play with. Let's get cracking.
 * YES.

Captain Hammer and Penny never had sex
The only reason for me thinking this is there was no sex scene, honestly. And Captain Hammer seems the kind of person who would assure everyone of his sexual escapades (see: "Everyone's a Hero"), even if they didn't happen. In "So They Say" he's just thinking about the second time because he's never had a second time. Not a perfect theory, but...
 * I actually thought this was true. Penny, shy and with a sad past, doesn't seem like the kind of girl who'd sleep with a guy on their second date. Sure, Hammer tells Horrible he intends to sleep with her, but Penny has a say in it too. He only wants her for sex (and to stick it to Horrible) and the only reason he's still with her in Act III is that she's holding out on him--long enough for him to begin to want her badly enough for a second time. During "Everyone's A Hero" Penny looks shocked and leaves when he blatantly lies that they "totally had sex". In fact, if they had had sex, Penny would already be disillusioned (there's a reason he only has sex once per woman).

Captain Hammer really cares about people.
Love Potion Number 10 from Horrible Turn made him love everybody like it was supposed to, hence the hero-ing and the "inspirational" speeches, but he's too big of an idiot to show his love in a rational manner.
 * That's not how it worked, though-- Love Potion #10 was supposed to make everyone love each other because everyone took it; it's solely inward, and thus it only affected others.

The Evil League of Evil is well aware that Horrible only killed Penny by accident
Like Captain Hammer, they were also reading his blog. They knew that Horrible would never kill Penny; in fact that might be the reason why they were reluctant to let him in, being Genre Saavy about such tropes Love Redeems (which is why they asked him to kill someone, to ensure he has some form of dedication to the job). However, with Penny dead, Dr. Horrible becomes a man with nothing left to lose, and nothing that can keep him human; the perfect villain. They let him in the League in a heartbeat.

The Evil League of Evil are all IneffectualSympatheticVillains
This creates an odd sort of tension as each tries to exaggerate about his or her evil while at the same time worrying that some other guy will find out they're spewing a load of hot air. Thus, ironically enough, Dr. Horrible is the most, well, horrible person in the League.

The members of the Evil League of Evil were like Dr. Horrible once
They were all outcast individuals who may have done questionable things, but they did have some degree of humanity, (or horse-ness). However, one bad event in their lives made them the feared force of evil they are today. Still, all of them wonder why they feel so empty inside, and what-could-have-been.

Horrible created Captain Hammer.
Yes, I know, it's not terribly original, but it does explain why Hammer focusses so much of his Super Dickery on Horrible; he resents his creator. His poor social skills are simply due to inexperience-- all that he knows about being human, he learned secondhand, mostly likely from movies and television. His self-loathing as an unreal "thing" also leads him to treat others like trash (to make himself feel better) and sleep around (to overcompensate for not being a "real man".) That therapist is going to have a lot of work on his hands...

The New Australia is a ship.
Firefly-class, possibly (the ship in the background), but more likely a small colony ship. There was more detail here last year, but the Data Vampires apparently got to it.

The Evil League of Evil isn't as epic as they are made out to be.
A more specific version of the C-List Fodder guess above, the ELE mostly sits around chatting and making up Fair Play Mysteries, and gives ridiculous demands to pledges that they are unlikely to fulfill. When Doctor Horrible (the most competent applicant so far) seemingly completes his objective "kill someone or stop bugging us" (which they moved up to and gave him an ultimatum of once it looked like he could seriously pull off something like a Wonderflonium heist), they let him join their upper echelon (really their entire ranks) out of fear. Ironically, the minions' union is far more evil than the League itself, despite the greater powers of the League.

Bad Horse is the Pony from Hark! A Vagrant.

 * I lol'd

The series takes place in the future of The Incredibles-verse
What could turn present-day society against science to the point that a genuinely gifted inventor and doctor of horribleness apparently has no day job?

A catastrophe caused by a similarly-gifted and extremely unhinged inventor in the past, perhaps...

Mild mannered Billy is Dr. Horrible's secret identity!
It all fits! You never see them in the same place, they both talk idealistically about a better world, and Billy seemed to drop off of the face of the Earth when Dr. Horrible got serious about the ELE.


 * ...You're kidding, right? Cause if not...

That one guy who is really obnoxious and wears a shirt with a hammer on it is Captain Hammer's secret identity!
I know, I know, that dude is so prissy, but they are both cheesy and self-absorbed, both claim to date Penny, and they are never seen together.

This is all just a way for Joss to make money during the writer's strike.
I mean, those theories about it being the premier of Neil as a villain seem a bit far-fetched. This is just my two cents.

Penny is a grown up version of Utena from Revolutionary Girl Utena
Listen to Penny's song and you'll get where I'm coming from. In this universe, Anthy never succeeded in finding Utena. Utena began to become a pessimist until she saw the homeless suffering and used this to fill the gap she lost when she gave up her 'prince' role. Her fleeting wish for a prince is what drove her to blindly accept Captain Hammer. Also, red hair is pink in anime.


 * Not always true. See Asuka Langley Sohryu (Neon Genesis Evangelion), Yoko (Gurren Lagann), and Dextera/Sinistra (Kiddy Grade)

Penny is Dead Not Sleeping
Hear me out. This is the Horrible Turn universe.

She was initially a Doctor Horrible fan, and curious about who he liked. She watched the song "Laundry Day," but the actual blog was just him singing in front of a camera, no footage from the laundromat.

She helps the homeless in order to do her part in making the world a better place.

She is affected by Love Potion 10 when she meets Captain Hammer, and thus falls in 'love.' She doubts him, but decides that she "believes there's good in everybody's heart." Ironically, this is the point where she stops watching his blog and thus doesn't learn who the girl from the laundromat is.

Her doubt intensifies with "Penny's Song," but when she's about to turn to Billy, Captain Hammer comes in with the good news and she realizes she has to be with Captain Hammer. Still, she curiously looks at the blog when Captain Hammer claims to be "too busy" and everything crashes down on her.

Love Potion 10 is an enhancer, but it can only do so much. The spell was broken, and she sent a message telling him who she was and asking him to come to the laundromat to talk over some frozen yogurts, but he didn't check the comments since he was busy making the Death Ray at the moment. In "So They Say," she wonders if she should just go with Captain Hammer and help make the world a better place, especially since Billy isn't coming. She finally decides it's for the best, as long as it's for "A Brand New Day."

However, she cannot believe she used to like him when she watches "Everyone's A Hero" with the Potion useless, and thus walks out. She knows about 'Billy Buddy' during "Slipping," but doesn't go out to stop him because she's pretty angry at Hammer too, but starts to go to stop him when she realizes he doesn't want to do it.

She takes no action during the scene with Hammer because she realizes the gun won't hurt Billy, but instead Hammer. When the last words came along, I'm gonna go with the "verify Dr. Horrible as a villain" theory.

Captain Hammer is a grown-up Warren Mears.
He could easily have survived, and because of Season 8 we know he did. He was put back together later by the same magic that gave him super strength and Nigh Invulnerability, or got a new set of orbs and got healing from a different source, and then blocked out any memory of the pain. More than likely, he actually couldn't feel pain because of the spinal fracture, and a section of his soul being ripped out of his arm by  was a type of pain that doesn't have to be transmitted through the nerves. He is a huge Kavorka Man, and is into fame, money, and women but has next to no charisma so the fame is something he could only keep in Billy and Penny's town, and the whole women thing never really works out. One of the most important similarities is that. It's quite possible that, assuming they take place in the same continuity (or even different dimensions in the same 'verse), Warren eventually became Captain Hammer, Corporate Tool. He may even have been taunting Doctor Horrible because he gave up on ray guns years ago, and Little Billy's still playing with nonlethal zat guns.

All women are doomed to evil in the Horrible Universe.
Basically everything that any female does ends horribly, no matter their intentions. The Fan Girls are so over the top that they turn Hammer towards more bashful girls, i.e. Penny, thus causing  The reporter who Dr. Horrible spells his name for is female and probably is the main source of information for newspapers on the story, thereby cementing his position as a villain. And worst of all, Penny, in her attempt to befriend a guy she met at the Laundromat, inadvertently causes him to fall even more in love with her and become all villain at, especially the line "Captain Hammer will save us."

Penny and her parents were in a boating accident. The parents didn't survive.
According to Penny's prequel comic her parents are dead prior to the events in the movie. During "My Eyes" She has the line "Just when you feel you almost drowned/you find yourself on solid ground." She also refuses to get into the paddle boat with Captain Hammer. During "So They Say" she has the line, "After years of stormy sailing have I finally found the bay."

Dr. Horrible will attmpt to clone Penny in the sequel.
Word of God says Penny is Killed Off for Real. But they also said that they intend to bring Felicia Day back for the sequel. The only way I can see that workig is for Billy to create a Penny clone... that averts Genetic Memory and develops a personality completely unliike Penny's. I expect some Cloning Blues.

The show is exactly what it appears: the story of a guy who achieves his goal, but it's all for naught because of the price he had to pay to get there
Yes, I just Wild Mass Guessed that the story is exactly what it appears. Not a "what if" story in Billy's head, not a parallel to high school, not Penny secretly being a villain or Billy/Horrible being two people, just exactly what it looks like it is. Oh yeah, I went there.

Dr. Horrible got into the ELE
...Not because his death ray malfunctioned and hit Penny, but because Dr. Horrible killed Billy. Of course, this only actually works if we accept the hypothesis that Billy & Dr. Horrible are two seperate personalities...

Dr. Horrible is an alternate universe Dr. Insano
He's a generally good guy who turns into an insane genius mad scientist when he dons a lab coat and goggles...he was driven insane after being rejected by the girl of his dreams...he is two different personas in the same body, the evil one taking over in the end...Which would make Captain Hammer an alternate Linkara.
 * SECONDED.
 * Wait a second. So Linkara's a Jerkass?
 * Well, Linkara and Captain Hammer are so utterly and completely DIFFERENT it kind of works...Linkara's a nice, feminist, nerdy guy with a decent brain and Captain Hammer is a Jerkass, womanizing, buff idiot. It could be possible, in a weird sort of way, that the they are completely opposite from their alternate universe version.

When he was younger, Dr. Horrible tried to get into the Heroes Guild
Unfortunately, scientists (aka "smart people") are only allowed to be Mad Scientists, and he was rejected. This led him to rejecting ALL of his previous "heroic" ideas except for the "not killing" thing. There really is no proof for this, but I suppose that's why it's here in WMG. ^_~

"Captain" is actually Hammer's rank
In a world with an ELE-like organization that clearly has a hierarchy of some sort, there would have to be a counter-organization. The organization is a militia of superheroes. The higher-ranked ones (like Captain Hammer) are the ones that get sent out to deal with the major threats, like an up-and-coming ELE member. Johnny Snow would be lower-ranked. Also, now that Dr. Horrible is officially in the League, it doesn't matter that Captain Hammer goes into therapy, because now his new nemesis (and thus the Big Bad of the sequel) will be higher ranked. A general or commander, perhaps.

Captain Hammer is gay.
I don't think I've seen this one yet, although I'm surprised. Given his sudden non-sequitar description of the "gently wafting" curtains, and his tendency to brag about sex with women to assert his masculinity, it only makes sense he's in the closet.

Captain Hammer secretly admires Dr. Horrible.
"...everyone has villains they must face/they're not as cool as mine..."

Captain Hammer is gay and secretly admires Dr. Horrible.
I know I am making this up but here goes. Captain is in the closet as said above and flirts with every girl he sees and brags about sex to appear straight. We already know he only wants Penny because Dr. Horrible does. This could be explained in a number of ways to support this theory. 1. Dr.Horrible wants Penny, I have Penny. I have what he wants. 2.He could be Jealous of Penny and wants to taint her in his crush's eyes. 3. Dating by proxy. 4. Gleen information. 5. Some combination of previous four. He flirts with every cute girl but does not pay her special interest until after he sees Dr. Horrible's concern when she is thrown in the trash. Dr. Horribles blog would confirm it for him. He deliberately came to find out about her laundry buddy because he knew from the blog that it was Dr.Horrible. He takes an interest in the homeless not to impress Penny but to imitate and one up her. If you believe he never felt pain before than he could be beating him up as a form of contact and not fully understand what he is doing to him. Basically he has a crush on Dr. Horrible and communicates it by stealing his crush, beating him to a pulp repeatedly, and taking an interest in the homeless. If you believe in love potion ten I can take this theory further. He joined the math team because he had a crush on the captain Billy then was too much of a coward to show up for multiple reasons including that he is an idiot and he couldn't face Billy. He tries to share Billys interests but doesn't understand like LP 10. He fakes disinterest. He wanted to go to Australia with Billy. He drinks the potion because he does not understand Billys real goals and thought it would complete the plan and thought it would magically make Billy like him as it would have if Billy did not drink the antidote before hand. He dislikes Wade for being close to Billy. He has no real interest in Kitty but dates her anyways for the same reasons he later dates Penny. He then decided to become a super Hero in order to impress Billy thinking he was into that stuff because Kitty was.

The sequel will end with Dr. Horrible killing the entire ELE.
Everyone seems to assume that there will just be one sequel that will resolve everything. I think a trilogy seems more likely. The second film will show Dr. Horrible’s further fall. Right now he’s only lost his ideals, but now he will regain them in a perverted way. Rather than trying to destroy society and rebuild it, he’ll be a Woobie, Destroyer of Worlds, bent on euthanizing the planet. The ELE, being Punchclock Villains, more interested in making money and sowing some limited havoc, will be seen as “unworthy” of him, and thus he’ll Kill'Em All, causing Moist (now his side-kick) to turn against him and go to Captain Hammer for help. Meanwhile, Captain Hammer will realize that he was wrong to use Penny, having never loved her, and that had he simply left her alone Dr. Horrible never would have become so corrupted (she might even have turned him good). Because of this he feels partially responsible for what Dr. Horrible is doing. This ends on a cliffhanger, with the two finally ready to square off.

Captain Hammer's first name is Jack
Because, hey, why not have another Captain Jack? Also, the pun is too delicious.
 * Two puns in one name!

One of Dr. Horrible's goals is to improve the American diet.
This just occurred to me today. I originally took his line "to the point where I don't know/if I'll upset the status quo/if I throw poison in the water main" was just a hyperbole, but he may have actually been commenting on American's drinking too many sodas and no water.

Dr. Horrible is a genius.
And if he didn't have his Breakthrough before the start of the series (which would make him a Hoffnung), then he definately did. His inventions, if he had the Breakthrough earlier, would be his Wonders, and the death ray malfunctioned not only because it got damaged from the fall but because Captain Hammer grabbed it. Moist would be Horrible's Beholden. It's also possible the Evil Leauge of Evil could also be a genius program. Or a faction of the Lemurians trying to make a comeback.
 * Alternatively, he catalyzed sometime during Brand New Day, making him a Neid. This fits with the fact that the Death Ray is obviously a Wonder, which explodes due to Havoc when Captain Hammer handles it. The obsession with getting revenge on someone fits nicely with the Neid template.

Or maybe he's a Spark from Girl genius?

Moist and Penny have history
Whenever Penny expresses an unhappy past, it involves water. My theory is that Moist, before he was depowered, or a more powerful realation of his (father) sunk Penny's family boat, leaving her the only survivor by happenstance.

Captain Hammer is a Lighter and Softer AU version of the Comedian, from Watchmen
Both are superheroes who aren't even slightly heroic, and both are implied to only fight crime because it gives them a chance to hurt socially acceptable targets. Both show tendecies to kill their enemies for no real reason. Both are misogynists.

Captain Hammer is Charlie Brown.
He started dying his hair to look more manly and less bald, and started beating up the people like Lucy, who liked to think too much for their own good and ruin others' chances at happiness (why'd Doctor Horrible have to try and pull the Superhero Memorial Bridge out from under him?)

Captain Hammer bought a handful of random clothing and put tracers in it to find out who was stealing his clothes from the dry cleaners.
Unfortunately, this time they just stole his reciept, so now he's stuck with four sweatervests.

Captain Hammer is a fan of The Fairly Odd Parents.
[Exaggerated Bavarian accent]You'd think without the sleeves it would be less of a sweater, but it is actually more![/accent]

Groupie #3 is gay.
He'll "do the weird stuff", speaks with a lithp, and his part in "So They Say" follows the anchorman's "Next up, who's gay!"

Groupie #3 is gay for Hammer.
Same as above, but with Single-Target Sexuality and minus the lisp thing.

Neither of the above guesses are wild. Now for an actual WILD guess...
Groupie #3 is straight and is pretending to be gay for Hammer out of a misguided belief that it will help him score with Groupies #1 and #2.

Bait and Switch are a brother-sister Police Sting unit.
Their power may or may not involve being able to change into each other.
 * They're actually shown in the movie, with Moist at Everything you Ever. Two girls.

The entire show is the tale of Barney Stinson's first suiting-up, as told to his blog.
He exaggerated the details, pushing his hippie persona up to a Deadpan Snarker and his awesome persona up to a Mad Scientist. Shannon is Penny, naturally -- in his mind Barney escalated her betrayal to. The guy in the suit is Captain Hammer. And the big suiting-up scenes of both works are practically identical. "A thing..." leads directly into his tears just after cutting to black.

The sequel will presumably cover the last bit of Barney's tale, eight years later.

Finally, Commentary! is set entirely in MacLaren's, and is actually sung by Barney's friends as they respond to his story.

Penny was actually killed by Buffy.
The events of the musical take place in...let's say between seasons 3 and 4 or so, you decide. Penny was actually a demon, impersonating a kindly human female. She was trying to get a homeless shelter built so she could eat people "no one would miss." This demon wasn't particularly powerful physically, which is why she jumped at the chance to get involved with Captain Hammer. Sarah Michelle Gellar is actually in the crowd in Act III -- you think it's just a cameo, but no. She's wearing a wig and sunglasses, indoors. She's faced this demon before, so she didn't want it to recognize her before she struck. Penny left the stage as Captain Hammer sang about his greatness because she either suspected the Slayer's presence, or wanted to smaple the homeless-people-buffet at the back of the crowd. As Doctor Horrible and Captain Hammer are "fighting" (WAAAAAAAAAAAAAY!), so are Buffy and the Penny-demon. The Death Ray explodes, a piece of shrapnel embeds itself in the wall near Buffy, she grabs it, yanks it out, stabs the Penny-demon with it, quips about it, and leaves. Doctor Horrible turns around, and sees the demon dying, still in its human disguise, and no one is any the wiser. This can easily tie in with the "Captain Hammer later becomes Caleb" theory.

A version of Doctor Horribles Sing Along Blog exists in the world of The Big Bang Theory.
Albeit not as a film, but as a cartoon drawn and written by Penny for Leonard, featuring a caricature of Leonard as the Villain Protagonist Main Character and a Friend to All Living Things Purity Sue with her own first name (although with a considerably different personality, wether this is intentional or not) as the Love Interest. Captain Hammer is a portmanteau personality of several different other ex-boyfriends of her. Bonus because Moist is played by Simon Helberg, who also plays Wolowitz in The Big Bang Theory. Penny intentionally left out a Sheldon-like character because she could think of no non-insulting way to present him, and she left out a Raj-like character because she doesn't really know him.
 * Surely, Sheldon is Bad Horse in this scenario? Elitist, socially inept (presumably it's hard to interact with people when you're a horse), and with all sorts of rules Horrible/Leonard have to meet. No clue on Raj though.

Doctor Horribles Sing Along Blog is a vector for SRMD
Seriously, am I the only one who watched it and got the urge to take over the world?

Dead Bowie is the David Bowie from the Buffyverse.

 * Ziggy Stardust and the Spiders From Mars made a stop in Sunnydale (or maybe Cleveland), and things did not go well.

The world will end about 2 days after the last images of the show
Think about it.
 * Don't worry. Captain Hammer will save us...

The purpose of this show was to show the reality of the relationship between Lex Luthor and Superman
Think about it. Superman/Captain Hammer is born with endless power. He has never felt pain or fear, and he is spoiled by the universe. He's not going to be a good person; he's going to be a pathetic jerk who is convinced that he can do whatever he wants, and who upholds the status quo because it's easy and people love him for it. Meanwhile, Lex Luthor/Dr.Horrible has nothing but brains and money, coupled with a desire to change a world enforced by a superhuman. He has to be a strong person with real goals and ability because he has to change the world with nothing to go on but what he makes for himself. Only in comic book land is Lex Luthor evil and Superman good; in the real world, or in Dr. Horrible, the roles are reversed. Dr. Horrible is a villain and evil, but is not a "bad guy".
 * Wait. The man who can go into Hell itself uncorrupted is evil, but the guy who goes into restaurants and gives (fiscally) poor married waitresses 30 minutes to decide "have sex with me for millions for a weekend or not" and then ditches before they can decide to give them gnawing guilt for years is a good guy? Oookay then.
 * We all know that Superman Is A Dick, and we have the comic book covers to prove it.
 * That would give new importance to "the hammer is my penis."
 * "Not become corrupted" doesn't necessarily mean he is completely pure. In fact, it could mean the exact opposite: Superman is already as corrupt as he can get, and Hell has no effect on him. But that's speculation for another series entirely...
 * Or, Lex Luthor could have paid for some nice Anti-Superman propaganda

Dr. Horrible isn't the Well-Intentioned Extremist we think he is.
The first clue is when he says the world is a mess "and I just have to run it". Not "clean it up" or "fix it", just "run it". Secondly, the fact that he makes a death ray, and proceeds to fire it randomly in a crowded room. Third, notice that in "Slipping", when he gets to "all the cash, all the fame/And social change" he nods in an odd way, as if thinking "oh yeah, nearly forgot to say that bit" -- social change is not his agenda and he had to remember to say it to throw the reporters off guard. Might also explain why the explosion of energy still caused the usually invulnerable Hammer pain despite seemingly not physically damaging him (as it might work by severely disrupting the body's electrical or other systems, rather like a stun gun would on a lesser level).
 * He fired into the air or the ceiling more than the crowd. Still, good point.
 * Firing at the crowd, especially with reporters in the room, would blow his cover. Ceiling pieces falling would provide the illusion of accident.
 * It's entirely possible that since he modified it from a Stun Gun, the Death Ray only affects organic material. So by firing it at the (presumably non-organic) ceiling he wouldn't be doing any harm at all (except maybe some scorch marks), just putting on an intimidatingly flashy show.

Dr. Horrible/Billy's last name is actually Nail as in Billy Nail or William Nail
When he's singing "Hammer meet Nail" in "Slipping" he is really referring to his civilian last name (even though it remains a bad metaphor). Also, all of the "Billy Buddy" stuff is just "Billy, buddy" as in "my buddy, Billy" and not a reference to a last name. His last name being Nail is also a large influence in his choice of nemesis, aka Captain Hammer. Very super hero/villain comic book genre fitting for an arch nemesis to have a name befitting the relationship.

Each of Billy's metaphors fits Doctor Horrible perfectly, and vice versa
On first viewing, you would be forgiven for thinking both Billy and his Doctor Horrible persona are not so great with words, but the truth is, every apparently failed metaphor made by one persona fits the other pretty darn well. Billy's speech culminating in "cut off the head" of the fish and of society is exactly Doctor Horrible's goal. Duh. But then you get to the other apparently failed metaphors, and you realize that the same logic applies to them all. When Doctor Horrible sings, "Hammer, meet Nail," he's talking about Captain Hammer meeting Billy, and doing as hammers do: pounding him down. This leaves us with the pie metaphor. This one, if you recall, is spoken by Billy, and could refer either to Captain Hammer - ostensibly - or Doctor Horrible. What this seems to mean is that the upper crust of the pie is Doctor Horrible -- our first impression of the Bad Doc is him in his Horrible persona, laughing evilly -- only for us to learn that under that persona is a shy, quiet guy named Billy who can't pluck up the courage to talk to a girl; yet, beneath that layer, so Billy tells us, is more Horrible: Billy/Doctor Horrible is Horrible at his core.

Moist will be the protagonist of the sequel.
Seeing that Dr. Horrible has indeed become a villain like he wished for but  and is thus mentally unstable, will try to either defeat or bring him back to the not-so-dark, but not-good side.

Dr. Horrible is doing the blog as part of his application to the Evil League of Evil.
This would explain why he's giving away enough details for Captain Hammer and the police to stop his in his plots, it's to show Bad Horse that's he actively being an antagonist and is dedicated to being a top-notch villain. Couldn't tell you why he sings on the blog though.

The final song (Everything You Ever) is not about Dr. Horrible mourning Penny's death as he becomes part of the Evil League of Evil.
I didn't come up with this theory, but it's about him realizing that he does not feel anything for Penny after she died, and he is surprised that he feels empty rather than sad as he becomes a full-time villain.

Bad Horse is Black Beauty.
He faked his death at the end of the book and formed the ELE to revenge himself on those bastard humans.

Dead Not Sleeping is Dead Bowie.
He watches Doctor Horrible's video blog! It would have been like a dream come true if Doctor Horrible had found out about it before his induction. He may also have nominated Doctor Horrible for League induction, based on his inventions and potential.

Moist is more "badass" than he realizes.
Think about it. He's wet. Perpetually, soaking wet. If he were to save all of the, can I assume "water", he's ever sweated, he'd have enough water to flood the city. That's gotta have some effect on his "most badass" comment.

Captain Hammer's real name is Maxwell Edison.
He took the name Captain Hammer because The Beatles inspired him to change the world for the better. The reason he chose such a ridiculous song for a superhero's name to originate is because he's a somewhat oblivious Jerkass, and either didn't realize that Maxwell wasn't the protagonist or didn't bother listening to the lyrics themselves.

The story is set in the same universe as Empowered

 * Specifically, several years earlier. Emp (still a college student at the time) was there when Dr. Horrible had a car thrown at him; noticing how innefective it was inspired her to write an entire paper debunking it.
 * More importantly, Captain Hammer will eventually dye his hair, promote himself through the vaguely-defined ranks, and go right back to hero-ing as Major Havoc. Billy, meanwhile, will have developed even more personality problems, and now spends his nights cleaning up Dr. Horrible's mistakes... as The God-Damn Maid Man.

Everything that happened happened. And nothing more.
Now, bear with me here, 'cause I know it's kinda crazy: Nothing was imaginary. The final act really happened. Dr. Horrible and Billy are the same person, not two warring personalities. How so much of the fandom takes assumptions like those as fact so unanimously, I have no idea.

Dr. Horrible, Billy and Captain Hammer are the same person
Billy is the main personality at the beginning and he is trying to ask Penny on a date without 'Captain Hammer' ruining it.

Everyone was faking their blindness to Captain Hammer's many flaws.
We don't get a very deep look at how people react to Captain Hammer, but when people seem pleased and interested in what he's doing, it's after Penny has started trying to set the jerkwad's powers to good use. Prior to meeting Penny, Captain Hammer was considered just as big a nuisance as Dr. Horrible by the everyday people and police that had to deal with the consequences of him being too busy showboating to actually catch any criminals or pay attention to minor issues like a runaway van. Captain Hammer was completely unaware of this because his perspective is godawful and Billy already knew his arch-nemesis was a tool. Penny never actually thought Hammer was a decent guy, she was just hoping maybe a positive influence might make him less of a Jerkass and perhaps lead him to doing some actual good with his powers. After the fiasco at the homeless shelter, nobody's going to put up with Captain Hammer's crap anymore and he'll remain a total wreck.
 * This makes a lot of sense in the context of Moving Guy's comment that it's "about time" Hammer cleans up the streets. Clearly, all his effort has been put into fighting supervillains rather than anything else, even normal criminals; knowing Hammer, he probably fought them even when they weren't doing anything, causing a lot of collateral damage.

Moist somehow sabatodged Dr.Horrible's freeze ray to stop working after a certain amount of time and is the real winner.

 * Moist kmows he will never get into the E.L.E. afterall he has no special skills but realises he will benefit from Dr.Horribles sucess. Judging from his blog to Jhonny Snow and his reactions to Moist suggestions Billy will just back out last minute, and maby blow up Caption Hammers statue or something to save face, instead of actually going through with his plan. Moist sabatodges his freeze ray hoping that if he wusses out, the freeze ray will run out of time, and he'll be forced to shoot Captain Hammer as a reflex. It doesn't work that way but he's not complaining.

The series actually takes place 10,000 years in the future.
Somehow people started getting super powers about ten years from now and then the war on nerds started because stupid genre savey people figured that nerds would become evil. Naturally this means that it might as well be illegal to be a scientist. As a result there is no legal scientific progress. This means it might as well be modern day unless you are in league with the super villians. People don't bother typing all five numbers so they stop at four.

The songs in Dr.Horrible are 90% true if misheard but disclaimers should be taken seriously.
Disclaimers: Thats the Plan, we swear, seems, think... Everything in future tence in laundry day is just part of his plan. Things are not always as they seem. Caprain didn't stop the van instead opted to crush Penny into debris.

Along with the Evil League of Evil, there is a Good League of Evil
or, alternately, an Evil League of Good, which is full of Anti-villains and Anti-heroes. They fight for a better world, but have no qualms about "Evil" methods. The ELE is only dedicated to doing Evil (notice how Dr.Horrible is just robbing a bank when he gets in?). Billy just never heard of the GLE/ELG.

Penny is an example of Attractiveness Isolation
Possably a deconstruction or just the way it is usually used. Instead of ending up with the dogged nice guy who is madly in love with her and she has a crush on, she ends up with a jerk jock who thinks hes to good for her and she thinks might be pretty okay.

Dr. Horrible will try to bring Penny back to life in the sequel.
Dr. Horrible has a PHD in Horribleness. That sounds like the kind of thing that lets you bring people back to Frankenstein-esque life. Beutifully illustrated by Irrel of deviantart here-

Captain Hammer will be so traumatized by his experiences that he renounces superhero-dom and becomes a mystery writer
Well, if he could become Mal Reynolds, I don't see why not. Also, this does explain his love for the macabre.

The show takes place in the DCU.
Hammer is obviously metahuman, probably some member of the Justice League's bratty nephew. The Justice League put him in charge of one city to keep him out of their hair, since he's not bright or noble enough to be a functional part of the JLA. The Evil League of Evil is made up of Sympathetic Ineffectual Villains who don't fit in with the other, more dangerous villains, and Horrible's plan is to join up, pull off an evil plan to get the attention of heroes/villains at large, and eventually use the League as a stepping point to greater villainy.

Dr. Horrible/Billy are not nearly as incompetent as we see them.
Basically I figured this based on the fact that I don't think the Evil League of Evil would have considered Dr. Horrible's application unless he already had some credit. The real problem for Dr. Horrible is that Captain Hammer usually thwarts plans that would have succeeded, and sometimes, he just has bad luck, but all in all, without Captain Hammer in the way and his luck holding out, Dr. Horrible's actually a very competent super villain.

Captain Hammer is Metro Man.
They look similar, they both have super strength, they're both Jerkass "heroes" of a big city who enjoy taunting a protagonist scientist supervillain and eventually lose to them. Not sure how this timeline would work, but the similarities are quite striking.
 * YES. I am so glad I'm not the only one to think/see this. Perhaps the singing is just a manifestation of his desire to be a professional singer? *Runs with the theory* And this was when he was still a Younger Adult and more of a Jerkass than he is in Metro City. Maybe the crushing of Dr. Horrible and the physical pain were enough to make him somewhat more decent.
 * For the hell of it. Bernard is Horrible after he died his hair or something. Maybe Horrible was wearing contacts.
 * The real Bernard never changes his expression and Roxanne says "I didn't know you had feelings!" at one point. After all, Horrible/Billy say "And I won't feel a Thing."
 * And then Bernard was watching Megamind to see if he could be accepted into the Evil League of Evil?
 * Mega Mind was supposed to kill Roxanne his 'Penny' thus was rejected.
 * This is now this troopers personal cannon.

Dr. Horrible and Moist are Robespierre and Saint-Just.
Suggested in this Youtube Video.

The end of the third act takes place in hell
But not Dr. Horrible's like people expect, but Captain Hammer's. When he fired the death ray, it did more than just hurt him, it actually killed him, and now he's feeling pain that he can never forget, is reduced to a sniveling wimp, the entire world no longer loves him, his arch-nemesis has become the ultimate Super Villain, and his ticket to hurting Dr. Horrible is dead too. But what happened, after Captain Hammer's death, to Billy and Penny? Who knows?

Penny has super powers, and ironically is the only person who could have
She has the ability to shield, heal, and resurrect people, all while having naturally wavy hair. If she had discovered this, her costume would have been white with a brown leather corset, brown leather boots, and gold trim. She may even have unconsciously shielded Billy during the Hammer Assassination scene, which distracted the power enough to stop shielding herself.

Penny has super powers, and is the only person who could have sex with Captain Hammer multiple times.
The reason Captain Hammer has never slept with the same girl twice is because of one of the downsides of superhuman strength. Penny has super-endurance, which allows her to bypass this. The reason that is that.

Billy and Horrible are indeed two separate personalities, but Billy doesn't disappear, recede, or merge with Horrible; instead he is simply corrupted while Horrible sadistically enjoys the show.
During "Slipping", Billy starts out singing about his victorious ideals in a soft, smooth tone, but at parts he lapses into a deeper, harsher "Dr. Horrible" voice. Now, here's the funny thing... as he goes on, it's the soft, smooth Billy parts that betray selfish goals and confused priorities, while the deep, harsh Dr. Horrible parts remind him of what he was after to begin with, as if mocking him for it ("All the wealth, all the fame/And social change").

Billy actually is a doctor in at least one real field.
He was skipped at least three grades as a kid, he's 28 around the time of the show, and he clearly has quite a bit of genuine scientific knowledge that he's just too shy and awkward to make good use of, so it's possible. Just that between his supervillain aspirations and the anti-intellectualism of the setting, he ironically gets more cred out of fake Morally-Ambiguous Doctorate posing than he would for his real doctorate.
 * He uses a Morally-Ambiguous Doctorate because using his real doctorate in medicine would bring suspicion upon the past identity he changed his name to escape.

Bad Horse cannot speak or write English.
Hence why all of his letters and calls are accompanied by singing cowboys: they're translating his whinnies and scribbles into English for the benefit of the recipient.

The sequel will feature Johnny Snow in some way.
He comes off strongly as being Dr. Horrible's good guy counterpart (wannabe super, loner loser, amateur gadgeteer, incredibly inept), and it'd be kind of appropriate to in the sequel get the parallel story of a weaksauce superhero becoming a real contender. (And in my ideal world, he'd be played by Geoff Ramsey, for the uncanny resemblance to his comic depiction and the amusement of another well-known internet webseries being represented...)

Dr. Horrible's next invention will be a planet-wide cloning ray.
After all, in "Everything You Ever" he does say he's here "to make the whole world Neil."
 * Because of you I think of this every time I listen to everything you ever. 'sad song sad song sad song -Make the whole world Neil- no longer sad song because its too damn funny'

This fanfic is an entirely accurate description of what the sequel will be like.
http://www.fanfiction.net/s/5900067/2/Perfect_Stories Well, it is Wild Mass Guessing.

Moist is the real villain behind everything, and he set Dr. Horrible and Captain Hammer up.
Either as a spy for the ELE or, just as plausibly, for his own purposes as the only way he could move up with such lame superpowers to become a major player himself. Well, it certainly makes more sense than Penny, and it fits in much better with Joss Whedon's modus operandi of having seemingly inconsequential, even Plucky Comic Relief characters turn out to be way more powerful than they seem at first, than having the female love interest not really die would fit. (It also fits the "perception vs. reality" theme of the movie much better.) Look at the evidence:

The "he" that's "still not answering" is pretty clearly Dr. Horrible. It goes with the Half-Empty Two-Shot of Penny in the laundromat to show that Horrible is so deep into plotting Hammer's demise that he's neglecting/ignoring the things he should be paying attention to: Namely his best friend and his Love Interest who care about him. And when it comes to his inventions malfunctioning, we see both the parking meter and the muscle-reducing ray not working, and Hammer snarking "What does this one not do?", before he meets Moist, implying that his inventions have always tended to not work. And when combined with things like: him ignoring talking to Penny to steal Wonderflonium when the whole reason he wanted it was to finish his Freeze Ray and use it to... get the courage to talk to Penny; not considering that Hammer and the police might read his blog; not realizing the Freeze Ray takes time to warm up; not realizing that a serum that's Essence of Hammer might give him Hammer's mind as well as strength, and so on--the impression I get is that the reason Horrible's inventions tend to not work is because he's too short-sighted/impatient/one-track-minded and doesn't think things through properly. ...everything else in your theory is rather interesting food-for-thought, though.
 * In the prequel comic, it's heavily implied his father was a Soviet spy. Espionage and intrigue is In the Blood, perhaps?
 * For that matter, we don't know what job Moist had before becoming a henchman, other than it was at a large but nondescript office building, and he calls it "boring," "inconsequential and uninspiring," but not "low-paying." Although he lives in "a closet with a toilet ... a half-bath" and drives a "reliable car," he never complains about money and seems not to mind spending four dollars a minute spilling his guts to unnamed phone sex operators. It could very well be his former job paid well but required anonymity and a low profile, although it was also obsolete and unnecessary, like the job of a Russian spy analyst in America after the fall of the Berlin Wall.
 * Another possible clue: The names of the characters on Moist's double date with Conflict Diamond. The "conflict diamond" name could be a hint to the Love Triangle of Billy/Penny/Hammer having four points, but the character's name is Conflict Diamond, not Love Diamond (or even the more common - and more supervillainy - phrase Blood Diamond). Combined with "Bait & Switch," this could very easily be a Stealth Pun combined with a Brick Joke.
 * During "Bad Horse Chorus," it's not Dr. Horrible to whom the cowboy sings the line, "A murder would be nice, of course." In fact, that's the only lyrical line sung to or by Moist, not just in that song, but in the entire movie.
 * It goes without saying Moist is much more comfortable with murder - even of children and the elderly - than Horrible is. "Do I even know you?"
 * If he is a spy, he may also be a Double Agent. Dr. Horrible assumes Captain Hammer and the LAPD watch his blog because they were ready for him at the Superhero Memorial Bridge ceremony, but in the Emmy hack, Captain Hammer lacks even the most basic knowledge of computers and the Internet. On the other hand, in the scene immediately after Horrible's assumption, Moist is wearing a "NJ State Police" t-shirt. By the way, just who is the "he" who's "still not answering" when Moist is making a phone call during "So They Say?"
 * On that note, why did Dr. Horrible's freeze ray fail both times? The assumption is he's incompetent, but he's learning. Unless someone were sabotaging his weapons so they would take a second to warm up or shut down at inconvenient times. Someone he trusts. Someone who knows everything. Someone with keys to his apartment. Someone who could introduce something notoriously bad to sensitive equipment, something like... moisture.
 * Of course, for Moist to pull off all these convoluted plans, he'd need to be playing a pretty mad game of Xanatos Roulette, right? Not necessarily. Moist has something neither Dr. Horrible nor Captain Hammer have: a Crystal Ball. Or more accurately, an Hourglass, who can see a random kid in Iowa becoming president. A common question about the movie is why Hourglass doesn't warn Moist of the futility of Horrible's plans, with fan justifications ranging from You Can't Fight Fate to Not So Omniscient After All. But what if Hourglass did tell Moist what could happen with just a little push, and he, well, uh... pushed?
 * A couple minor nitpicks:
 * It's possible that this was originally supposed to be canon, and the character of Moist is The Artifact. It would explain the existence of Nobody Wants To Be Moist.

There's a happy ending.

 * It doesn't matter how much would have to be changed, or how much would end up being a love story. But there needs to be a Happy Ending. There just needs to be.

Captain Hammer really was becoming a better guy.
Wouldn't it be just like Joss Whedon to have Dr Horrible lose Penny and become truly evil whilst also stopping Captain Hammer from truly becoming a good guy? Knowing Whedon, he was probably going to lead a campaign of social change that'd solve every problem that motivates Billy and Penny would have broken up with Hammer and gotten together with Billy.

Wait, maybe I should delete this WMG before Joss sees it and makes it canon! Quick!

The not-so-good doctor is The Brain
They are both Affably Evil Anti-Hero\Anti-Villain Mad Scientists who believes that World Domination is the best way to make the world a better place, and are big time Woobies. how can a cartoon mouse be the same person as NPH? well, I have a few gusses...


 * The Brain and Doctor Horrible are AU counterparts of eachother. The Brain is just lucky enough that's with all the crap the world throw at him, AU Captain Hammer WASN'T one of them, and that his Morality Pet is a good friend as Pinky
 * The Brain decided that he would have a better chance to Take Over the World if he was a human, so he either turned himself human or builded a better Human suit. he was forced to leave Pinky in the lab (maybe the scientists wouldn't care of one mice ran away, but two may attract too much attention. maybe he needed him to keep an eye on another project (or, more likely, the next step of whatever his overcomplicated plan is). or maybe he couldn't turn pinky human\ bulid him a human suit and was afriad that someone might step on Pinky) and as a result got more and more cynical as time went. he started taking interest, and falling in love with Penny becuase he thought she would make a good Pinky substitute.
 * like the last one, but Brain's plan happend in one of those episodes that are inexplicably in another time period - this time, the year 1980. due to a miscalculation about the age differences between humans and mice, the... Turn-Mice-Into-Humans-Thingy turned Brain into a two years old toddler, and later adopted and given the name Billy. leaving him with his brilliant mind, but without any memory of Pinky or his life as a mouse. (if you consider the prequel comics canon)

What will likely be the plot of the sequel:
Dr. Horrible loses his passion for villainy and just gets more and more depressed, until one day he decides to quit the ELE, improve his freeze ray, and revolutionize the world of cryonics, since instead of freezing someone with incredibly low temperatures it just leaves the person stuck in a moment in time while the rest of the world keeps moving. Since they're all living in such a Crapsack World, everyone wants to try the procedure and leave the fixing of the world's problems for others to deal with. The thing is, the entire population uses the freeze ray procedure, and with everyone in the world frozen for one thousand years, the Earth is at a standstill. Everyone, except Dr. Horrible. Unencumbered by the sheeplike masses he so despised, he lives out the rest of his days mourning Penny, finally alone and finally the most important man on Earth. A long time after he's dead and gone, about four hundred years into the freeze, the process malfunctions and all people under its control die, and thus ends the era of the human race.

Billy is insane and hallucinated most of the movie, beside the blog
About two years before the start of the show, Billy experienced some sort of a horrible trauma, leaving him delusional and living in a made-up world of super-heros and Mad Scientists. the blog is basically him bubbling about "crimes", made-up super heros and villains ,singing at the camera and being kinda creepy (just imagine the opening scene in the real world, that's pretty creepy) mostly visted by people who thinks about it as Bile Fascination and Trolls (Such as "2Sly4U" and "Johnny Snow") who poke fun at the poor insane man. Moist was Billy's friend from before the trauma with a bit of a sweating problem that found himself having to play along his friend's delusions, fearing that telling him the truth will only make it worse, while subtly trying to make to stop the super-villain stuff (the murders he suggested in Act II were mostly to try to make Billy stop wanting to be evil). The non-ELE villians are simpilly "Moist" 's friends and the ELE are completely made up (the reason Penny heard about Bad Horse is because it became a Memetic Mutation in this world). Penny is mostly the same, but less of a Mary Sue and has a boyfriend who is also volunteering for Caring Hands. Captain Hammer was at first a made-up character - but after Billy learned that Penny has a boyfriend, he put him as Captain Hammer. the van robbery was mostly a hallucination, beside the Penny part. Penny wasn't really interested in Billy, but talked with him mostly out of politeness and pity. The Freeze Ray Noodle Incident was just him breaking into some dedication of a bridge with his prop, causing panic and almost caught by the LAPD. Penny's Boyfriend just came to the coin wash tell her they got the buliding and then left with Penny, he recognized Billy becuase he used to watch the blog. he rest of the Billy\Captian Hammer conversation wasn't real. All of "So They Say" was a fantasy too, the death ray being just a rifle. While Penny's Boyfriend did made the speech that Billy's mind turned into "Everyone's a Hero", it was in the name of all of the Caring Hands volunteers and was actually positive. nobody did anything in Slipping because... well an insane guy in a lab-coat and a rifle just started shooting wildly into the air and rambling about weird stuff, would you do something? during the shooting, he accidentally hit Penny (something his brain "translate" into "it was all Captain Hammer's fault") and before she dies - she mumble bunch of meaningless word, that, to Billy's wraped mind sounded like "Captian Hammer will save us". the guilt and grief on the death of Penny caused him to completely lose connection with the real world, dreaming about honor and fame while mumbling to his webcam - totally borken.

Billy/Doctor Horrible has borderline personality disorder.
It seems more likely than straight-up split personalities in my head. He shows many signs of BPD: dissociative, mood shifts (especially during Slipping ), unstable personal relationships and self image, unstable behavior, and idealization and demonizing of others (because honestly, Penny couldn't be that pure ). However, BPD can also lead to self-harm and suicide if untreated... doesn't exactly foreshadow good things in Doctor Horrible's future...

Doctor Horrible is Alternate Universe counterpart of Doctor Steel
Both wanted to change the society, both are mad scientists wearing cool googles.

Alternatively Doctor Steel exist in the same Universe
And guess who is going to show u for Villain Team-Up in the sequel.

WMG: Even more alternatively, [[Doctor Steel is future Doctor Horrible Going with theory that Billy and Dr. Horrible alle two different personalities it is possible that he could develop thirth that consumed the others or that they somehow merged. This new persona has viarous traits of both Doctor Horrible (mad scientist at the verge of world domination) and Billy (wants to make a world a better place) but also repressed his memories, creating fake origin about blowing up toy factory. This however resulted in them manifesting as longing to something else - just as Billy/Doctor Horrible misses, his new personality misses his happy childhood. Try pretenting this is singed by Horrible, espetially the second part, and you may understand where I'm coming from with that idea.

Dr. Horrible has a superpower
he's Nigh Invulnerability, but still feels pain. that's how me managed to survive getting beaten-up so ofen by a super strong Jerkass. and to add to it...

Dr. Horrible is an experiment to create the perfect "Punching Bag" for Captain Hammer Gone Horribly Right
the government looked for a way to suppress Captain Hammer's love for cuasing pain ,and so decided to Genetically Engineer a sort of a "Punching Bag" for him - a largly non-threating villain who will be able to take whatever CH does to him but still suffer from it. His Fake Memories were created in a way that made sure that he will have a special abhorrence toward CH and everything he represent, and will never stop trying to take him down - and the whole Even Evil Has Standards and Thou Shalt Not Kill stuff were programmed into him to minimize the dangers of intentionly creating a Super Villain. Too bad the scientists never thought about the Psychological damage that CH might do to poor Billy.

In 'My Eyes', the Penny/Billy duet, Penny can hear Billy, and knows he's there.
Forget the songs not being 'real' - she knows he's there, every time he's in the background and singing. She hears him singing - and her verses? She's countering his dismal, depressed, cynical outlook - his personally, not just as a characterized juxtaposition for the audience to cue in on. She hears him singing, and can't help but try to help - and, well, it comes out in song, of course!

Billy thought that he lived in a musical.
Every one of his songs was an actual song that he was singing. The other characters'? He was just making it all up. The line "arise and sing" from "Everything You Ever" was his reveal of his actual evil plan-- to make the whole world into a musical.

Penny didn't know that she was injured.
If you listen really carefully, while Billy's panicking, you can hear her say, "Billy? Are you okay?" She was in so much pain that her body basically shut nerves down to prevent her from feeling it; based on his scared expression, she thinks that he's the one who got hurt. Her "Captain Hammer will save us" isn't an expression of naiveite- it's an attempt to comfort her friend.

Doctor Horribles Sing Along Blog takes place in the same universe as My Little Pony
More specifically, My Little Pony Friendship Is Magic. Bad horse's evil plan was to rule the world and turn every single human being into a horse. When this failed, he settled for the smaller and more manageable ponies. Then, he chose a few specific people from the Evil League of Evil as 'special experiments." He turned the two highest in his favor into Luna and Celestia, while he turned the lowest into Discord. After a long series of genetic mutations, the normal ponies mutated into the pastel unicorns, pegasi, and alicorns we all know and love.
 * I love you.

Bad Horse owns and runs Dark Horse Comics.
The spin off comics they produced are his documentation on the various people involved in his business that he published for posterity.

Bad Horse can swordfight.
If he's so awesome he can sign a phone, this should be well within his ability to do, all he needs to do is hold the sword in his mouth, just like a certain Pirate.
 * Or just like Maximus.

The End of Act III is All Just a Dream.
Okay, so here's how it all goes down. Everything up to the point of the death ray exploding happened. Now, when the death ray exploded, Billy was knocked unconcious and began to imagine what 'happened' after, including. The thing is, HE got hit with the shrapnel instead of. So, Penny sees her laundry buddy Billy near-death and, saying as Captain Hammer has already run out of the building, decides to take matters into her own hands, not caring that Billy and Dr. Horrible are the same person. She gets him to a hospital just fine(because, let's face it, Billy is Made of Iron), and he survives, but is stuck in a coma. That said, the entirety of Billy getting into the ELE and such is pretty much the equivalent of an Adventure in Coma Land, minus the whole "what happens there defines if you wake up or not"-ness. Eventually though, Billy'll wake up, realize that  was All Just a Dream and may or may not end up dying from his injuries (though, him dying is doubtul, mainly due to the Made of Iron bit from earlier, this IS Joss Whedon we're talking about...)

Also, just because (and sequel-ness), Penny will watch the blog, and make a vow to try and make the world a better place for Billy so that he won't have to be Dr. Horrible anymore. From that point, the focus will be on her being a 'hero' to the city, and generally trying her hardest to achieve that goal.

The League is a front for somebody much worse.
It's actually ran by Dogbert, the reason it's never tried it's hand at world domination is simply because Dogbert isn't interested.