The Penguins of Madagascar/WMG

Skipper and his team are drag queens
Okay, I know it sounds crazy, but think about it. They are all males who live together. They seem to have a very strong bond, which according to Wikipedia is one of the factors. It could also explain why Skipper had a ribbon on hand and why Marlene came to him with advice about what she could wear (because they need to know what clothes women wear). Also, let's look at the fact that they get NO money from what they do and they need to fund it. They just save the zoo when they aren't doing shows and they like protecting people.

One of the leads is female...
Kowalski's DNA test was wrong; one of the team is female, just as Alice claimed. But the show won't ever reveal which one.
 * Obviously the penguins' frequent Ambiguously Gay behaviour is what convinced Alice one was female.
 * Kowalski made the machine. He could make it lie - most likely for him. "I also have a plus... obviously." Suspiciously Specific Denial? He says that and doesn't even look at his result.
 * The trouble with Kowalski lying with the machine is when it goes wrong. Alice says 'three males, one female'. If Kowalski lied for somebody, including himself, he'd know the machine was wrong. But then Skipper comes up the girl and Kowalski just swings with it. The only feasible option is that the machine went wrong and Kowalski didn't know it. After all, he wasn't expecting the power cut to give Skipper even a temporary minus, and Skipper would believe they're all males anyway.
 * If he can make shrink rays and time machines, he can make a machine which lies for him and tells the truth for the other three.
 * The whole joke of the episode rests on the idea that even the penguins have no idea if they themselves are male or female. Skipper accepts being female. Rico actually looks between his legs. Kowalski doesn't even look at his own result, he's so confident. It's a lovely idea but it's absolutely crazy that the penguins themselves don't know their own gender.
 * In "Love Hurts", Alice calls Private 'princess'. Maybe 'he' is the 'she' after all?
 * In "Operation Break-Spear", Kowalski blasts penguin mating calls at the lemurs, full volume. The only result is that Rico gets turned on to him. Or her?
 * In Parental Egg-stinct Skipper seems to be immune to Eggy's charm. However, he does fawn over the others cooing the egg. Private has said the best way to a women's heart is to sit on her egg. Maybe the results were right?
 * In Madagascar: Escape 2 Africa, Marty calls Private 'Miss'. Does he know something we don't?
 * Additionally, in the second movie, Private produces an egg to help with the illusion of being injured. Did he - she - lay it?
 * It's certainly not Kowalski who's the female. Look at Kowalski 'dancing' at the beginning of "Cute-Astrophe". No woman, straight nor gay, alive nor dead, would ever dance like that. Ever. Ever. Only a guy would mistakenly think that was cool.
 * Except Skipper and Rico, who are guys, really don't seem to like it either.

The zoo was supposed to receive a female instead of one of the leads, but there was a mix-up.
She's Chekhov MIA, and so she'll eventually be introduced as a Mary Sue parody who nearly replaces one of the team, only to be shunted off to much acclaim at the end of her introductory episode because Status Quo Is God and nobody's going to break up the Badass Crew. (On top of that, she'll likely turn out to be one of Blowhole's agents.)

Rico is a transfer from Hoboken Zoo
That's where he got the scar, that's why he's a psychopath, and that's why he's got no rank.

Joey's Ax Crazy bent is due to Medium Awareness.
To be more precise, he is aware that his gender is mutable for the sake of pouch jokes. You would be pissed off, too, if the Rule of Funny screwed over your body and hormones for the sake of comedic timing.
 * Oh yeah?
 * ...Are you suggesting Joey fell into the Spring of Drowned Kangaroo Doe?

The penguins are members of the OWCA.
Or at least Skipper is. He's just waiting for Perry to show up and spring them!

Skipper is running Madagascar in the online game Pandemic.
Hence the immense paranoia and reaction to the slightest hint of infection.
 * Also why Madagascar's so bloody hard to infect.

King Julien is a self-proclaimed leader.
Maurice alludes to this with one line in the movies; while Word of God places movie and series in separate continuities, that doesn't necessarily mean there aren't similar circumstances behind his rule. Any number of things could have happened to the previous leaders, and Julien simply stepped into the resulting power vacuum.
 * The previous leader was a female. Maybe even his wife.
 * If he was related or married to a high-ranking lemur but wasn't expected to actually wield power himself, that might explain why he's as spoilt and irresponsible as he is. It's possible that once he got the power, he wasn't sure what to do with it and went a bit off the rails.

Skipper and Rico fought in Vietnam and had their brains addled by Agent Orange
This is why Skipper's description of what happened to Manfredi and Johnson keeps changing; sometimes he remembers it one way, sometimes another. His fear of needles was due to the Viet Cong using them to torture him while in captivity. Rico suffered even worse, hence his inability to function in normal society. He could've been subjected to experiments by visiting Russian scientists and gained his ability to hold a seemingly infinite amount of items in his gullet at the cost of normal speech. It is possible that Dr. Blowhole was the one who orchestrated their torture, hence Skipper refers to him as his nemesis.
 * "Blowhole. King Rat. Officer X. These men, these "animals" must DIE."

Whatever really happened to Manfredi and Johnson gave Skipper Trauma Induced Amnesia.
Something horrible happened to those two, and Skipper witnessed it firsthand. While he managed to escape the same fate, he suffered a Heroic BSOD afterwards. All he recalls clearly about the incident is something happened, but he can't recall just what... so he tailors his recollection to whatever's relevant at the moment.
 * Maybe it has to do with what really happened in Denmark... or in Mr. Tux, when Skipper mentions that he once woke up in Kyoto on a bed covered with Deutschemarks.

Julien is a Transsexual
Specifically of the Female-to-Male variety. The other lemurs in the movies would obviously do whatever he told them to, which would include treating him like a King rather than a Queen. In the series, the other zoo animals allow him to pretend to still be an authority figure because he would otherwise have no way to maintain his desired gender identity and they are all nice like that.
 * Considering that lemurs are supposed to be matriarchal, it would be more logical for the lemurs to want a queen than to want a king, so this would make sense. Maybe they let Julien get away with ruling as "king" by deciding that they do still have a queen, just a crazy queen who wants to be called king instead. When Maurice refers to Julien in the movie as "self-proclaimed lord of the lemurs," perhaps he means the "self-proclaimed" part is in the implied gender of "lord," not the status itself. (Or, both.)
 * That way is not particularly up on widely-accepted transgender etiquette, but maybe they just didn't want to argue with the logic loop. Officially a female's supposed to rule, so he can only rule if he's female, but if he's the ruler he can do whatever he wants including declaring himself male ... Meh, either way they all seem to have ended up happy enough, and in a world where it's apparently fairly common to not notice one's own biological sex and Julien seemingly didn't know how to tell he was a mammal, you can't blame them. Also, he's comfortable enough in his gender identity to dress as a girl on occasion (in the second movie and in the episode where he and the other lemurs were being cheerleaders), so if this is true it seems to be working pretty well for him - then again, dressing in drag may not have the same significance when he normally doesn't wear anything. That and some other feminine behaviour on his part makes me wonder if he may actually be male-leaning genderqueer (regardless of his actual anatomical configuration), but since the only one who could confirm that is him, we'll never know.
 * An alternate to the "they are all nice like that" idea: maybe the other animals in the zoo don't realize that Julien is transsexual? Despite the fact that he's, you know, naked. I wouldn't put it past the rather anti-mammal penguins (who can't even tell their own sexes) to completely miss even primary sex characteristics in mammals. As for everyone else? ...Maybe they just don't look too hard?
 * Or, considering that they might have another transsexual animal in the zoo (Joey the kangaroo, and, if you look at the first entry on this page, possibly one or more of the penguins), perhaps by the time the lemurs arrived, the zoo animals had concluded that questioning the preferred gender of a female animal who's acting male will result in an excruciating amount of pain.
 * According to this article, female ring-tailed lemurs have an enlarged clitoris, so at first glance anyone not familiar with lemurs may not notice, even if you assume they can see through his fur when the viewers of the cartoon can't thanks to artistic convention. Also, male lemurs have spurlike claws on their wrists which the females don't, and Julien doesn't appear to have those - probably just due to simplified cartoon anatomy, but it leaves the possibility open. And Kowalski may or may not know, even if the others don't; when Julien claimed the duck egg was his, Kowalski was more concerned about Julien being a mammal than being male when saying it was impossible. Also might explain why Clemson in "Right Hand Man" automatically assumed the "king" must be Maurice or Mort, beyond Rule of Funny - he noticed the anatomy differences.
 * This probably wouldn't work with lemur anatomy, but I see room for a human!AU fanfic where the reason Julien doesn't want people touching his feet is because he's afraid someone will realise his feet are unusually small to belong to a guy. Speaking of fanfic ...
 * Why does he have all that baby-care equipment in his habitat in "Rock-A-Bye Birdie"? Because he has a uterus and the zoo is hoping to breed him. He's been lucky enough that the potential partners they've signed him up with accept that he doesn't want to actually be pregnant. And come to think of it, he does have a teeny bit of curve around his hips (female lemurs shouldn't, but a couple of the females on the show, e.g. Marlene, do have a touch of curve, and with his constant dancing it seems unlikely to be regular pudginess) and in an unguarded moment in "Lemur See, Lemur Do" he demonstrates a very Girly Scream (since he has no access to testosterone shots, his male voice must be down to practice, and the shock might have made him forget to keep it up) ...

Doctor Blowhole isn't Skipper's nemesis -- he's Kowalski's, by virtue of being his Evil Counterpart.
Whether he realizes it or not, Doctor Blowhole is much better at rattling Kowalski than he is Skipper. Skipper may be the leader, but aside from assuming Blowhole having a fin in various plots against the team, he's rarely shaken by the Mad Doctor's posturing and scheming -- not like Kowalski. Kowalski takes the doctor's antics much more personally... and the main reason? "Kowalski: "Why do the bad guys always get the good stuff?!""

Doctor Blowhole, therefore, represents temptation and the idea that Mad Science is AWESOME, with the freedom to do whatever one wishes in the name of SCIENCE! Something that doesn't faze Skipper half as much as it does Kowalski, because that's not something that particularly appeals to him the way it does his Idea Guy. Kowalski only wishes he had the sort of freedom the morally unchained and unhinged Blowhole enjoys -- but, being one of the good guys, he's not able to cross those lines. Simply put, Kowalski's jealous, fully aware of it, and pissed off because of all the uncomfortable lines of thought that raises.
 * Agreed.

Rhonda will return.
Marlene may have played right into her flippers, but she'll still have a score to settle with the little "rat". After all, Marlene did nearly get her killed, and in Rhonda's eyes wasn't a very good roomie. Plus, her return would open up the possibility of Marlene learning the truth about the penguins and Doctor Blowhole, though whether or not she actually winds up breaking into the Masquerade is still up in the air...

Marlene is a reincarnation of Marla Singer.
That's why she's hanging out with penguins.
 * It's also the reason why Marlene is a constantly happy Valley Girl and enthusiastic about anything. God wanted to show irony by turning her character around 180 degrees for her new incarnation.

Rico is a reincarnation of Rico Rodriguez.
Why not?

The Penguins of Madagascar is actually The Big Bang Theory told from the viewpoint of an Unreliable Narrator.

 * Skipper is Leonard.
 * Kowalski is Sheldon.
 * Rico is Wolowitz.
 * Private is Raj.
 * Marlene is Penny.
 * The Lemurs and the other animals are imaginations of the Unreliable Narrator's crazy mind.

I know this one doesn't really make sense. It just came to my mind that Marlene and Penny are somewhat similar characters. (Valley Girl, sort of.) Also, both of them hang out with guys they don't really understand.
 * Fred is Zack. Fred dated Marlene and Zack dated Penny, and both suffer from the exact same kind of stupidity.

Rico is a ChickBomb Gone Horribly Right.
Rico was hatched solely to become the test subject of a very secret experiment to create the perfect Super Child Soldier: a one-penguin army who doubles as his own armory. Raised from birth, his only source of stimulation (and the only sense of control he had over his environment) was whatever carnage he created. Mad Science gave him his Hyperspace Arsenal (the elevator and stairs were installed simply to make working on the lower levels easier), and he was constantly drilled, constantly tested, constantly fighting whatever his supervisors threw at him, no matter how horrible or mind-breaking it was.

They wanted a fantastic living weapon. They succeeded in that regard. But Rico became... well. Rico.
 * Optional twist: the scientist behind all this? Doctor Blowhole. Skipper stumbled across the experiment during one of their battles, busted Rico out, and they've been partners ever since. Skipper, for his part, finds himself torn between Defusing the ChickBomb or turning that semi-controlled chaos to his own ends. Kowalski may or may not know, or only knows part of the story; Private definitely doesn't know anything about it.
 * Another twist; Rico was the one who took out Manfredi and Johnson. Skipper has suppressed the memory in order to successfully work with him now he's mostly Defused.

The penguins are KGP agents.
Enough said.

Huffin and Puffin was pulled from US circulation because of a 9/11 reference.
Hans takes over the penguins' HQ and monologues about how he is in the heart of a major city with their weapons at his disposal. Nick probably freaked at the last minute and pulled the episode, never to see the light of day... except in Canada, and every country that dubs it.
 * And anyone who watches it on Vodpod (No, I'm not linking. I don't condone blatant copyright infringement like that unless there's a good reason. And Nick being too candyass to show it (like Kaboom and Kabust) is good reason to me.)
 * ... So you are condoning it?

Maurice obeys Julien out of pity.
Julien thinks he's the great king, but he's totally desperate without Maurice and Mort. Now Mort mainly obeys Julien because he loves Julien's feet, but what is Maurice's motivation? He pities him. (This is most obvious in "All King, No Kingdom".)

The penguins are a metaphor for the Open Source movement, especially Linux. The lemurs represent the big software corporations, especially Microsoft and Apple.
Why not?

Julien is married or was suppose to get married back in Madagascar.
Think about it. Julien makes a big deal about king yet he surrounds with people that couldn't care less about his title. Why not just go back to Madagascar where all his adoring fans are? Because if he went back, he would be force to get married. The new queen will get all of Julien's power since lemur have female monarchy, leaving Julien with nothing.
 * Or maybe it already happened, and he's already got nothing, which is why he's willing to live in the zoo. In exile, where nobody knows about lemur politics, he can still claim to be a monarch. Who's there to argue?
 * His instruction to Rico to deal with a girlfriend by obeying her unquestioningly might be a sign this way as well. Probably depends on how severe the usual lemur matriarchy is as to how much should be read into that.
 * Alternately, for those who buy into the Julien-is-a-Transsexual theory, perhaps he was supposed to marry a male lemur (assuming the lemurs let Julien get away with claiming to be male only because they still consider him to be a "her" and thus queen). The sheer amount of squickiness he'd get from that idea might be enough to keep him from trying to get home, even though presumably he'd still be the one in power.
 * Or, keeping with the transgender theory, maybe he didn't mind the idea of marrying a male as such but wouldn't do it because he was expected to get pregnant to provide an heir. That might explain why Maurice must have helped him leave; the idea of Julien reproducing is pretty horrifying, regardless of which biological parent he'd be. He was disgusted to find out where mammal babies come from; unfamiliarity with females, or denial due to fear of it happening to him?

Kowalski can actually read
Simply put, there is no way, even as absolutely brilliant as Kowalski is, that he could come up with his inventions without ever being able to read. Skipper probably told him to always pretend not to know how to for a strategic reason (e.g. anyone gathering info on the penguins would get that piece of information wrong). Evidence for this is that he can operate his mini-computer / voice synthesizer perfectly, and get it to say whatever he wants to.
 * Alternatively, he can't read now, but will learn how to by the end of the series as some much needed character development.
 * It's strange though, but Private seemed to be able to read in the episode "Tagged", when he was reading from that field guide. So if he can read, why shouldn't Kowalski be able to?
 * Because they only teach penguins how to read in British zoos. You know the American school system, and it would be worse for animal education.

Doris the Dolphin isn't real
Let's look at the love lives of the penguins, shall we: Following this trend, it can be assumed that Doris the dolphin is a signpost, a statue, or even another doll.
 * In the movies, Skipper had Lola, a bobble-head doll. He even went as far as marrying her in the second movie. (Though on the show he did have Kitka for that one episode.)
 * Then we have Rico with Ms Perky, a Barbie-type doll.
 * Private, on the other hand, doesn't seem to share the penguin's lust of inanimate objects. His love interests have been Cupid, a lady reindeer on the Merry Madagascar special, and Shawna, a human veterinary intern. It's implied though that Private hasn't been with penguins as long, hence isn't as insane as everyone else. He's the exception that proves the rule.
 * Exceptions don't prove rules in the way you think that means. 'Prove' in that context means challenge. How dumb would it be for a rule to not-always-be-true-and-therefore-be-true? Makes no sense.
 * Kowalski also had a brief thing for Officer X's van before they were forced to destroy it in the line of duty.

Rico is a powerful psychic capable of creating any object with his mind
He hasn't actually ingested any of the stuff he spits out - he actually has the ability to cause anything he imagines to come into being and fire it from his mouth. This explains his Hammer Space Arsenal, and the fact that he seems to have a Context Sensitive Button allowing anything the situation calls for to just so happen to be readily available. If he so chooses, he can also store things in this dimension by putting them in his mouth.

The wishing well from the episode "Wishful Thinking" really did work.
At the end of the episode, we see that the elephant really had been to Paris. So apparently the wishing well really did work. Perhaps it's the result of a side effect of one of Kowalski's experiments that he himself is unaware of.
 * But Private's wish was to make it so that everything that had happened would un-happen, which would have included the trip to Paris. So, either the elephant picked up that bread and hat somewhere else, or else the elephant discovered the power of the wishing well by himself and took a trip.

Buck Rockgut would be no danger to the plans of Red Squirrel even if he was still around.
This is not so much a Wild Mass Guessing. It's rather obvious. Rockgut is paranoid beyond sanity, and completely incapable of logical thinking. Chances are high that if the Red Squirrel would act openly, Rockgut would suspect anyone else but the real Red Squirrel.
 * Hmm... talking about red squirrels, eh? Know who else talks about red squirrels?

Manfredi and Johnson are Skipper's old action figures.
Ever since he was a mere fledgling, he dreamed of adventuring with his own squadron. So he got a couple of dolls action figures and had various misadventures. This is why he claims that they suffered various gruesome fates that would kill a normal penguin: in one way or another, all of those stories actually happened in one form or another. Given Skipper's nature, not all of these adventures were just his imagination... Manfredi and Johnson probably went through the same sort of abuse BUSTER gets.

Doris is in league with Dr. Blowhole
All we know about Doris is that she's a dolphin, Kowalski records himself on DVD reciting love poetry about her and breaking into sobs, Skipper has had at least one dream about her which may or may not be based on reality, and Doris likes Kowalski but she doesn't "like him" like him. So, where is she, and why doesn't she "like" like Kowalski? Perhaps she's one of Dr. Blowhole's agents. (They're both dolphins. It makes perfectly logical sense.) She was sent to seduce the "smart one" of the penguins and get whatever info she could out of him. Her absence from the series could be for many reasons: maybe she found what she was sent to find and/or had to abandon the mission, and left; maybe Dr. Blowhole thought she was getting too emotionally involved and ordered her off the mission; or maybe she's currently involved in one of Dr. Blowhole's larger, more nefarious schemes. Quite probably the penguins have yet to learn that she's an agent, or else Skipper's "she doesn't 'like you' like you" line would have been something more like "she's evil, remember?" When/if she shows up (and it's quite possible she will, as the show is very fond of taking earlier episodes' throwaway gags and devoting a whole episode to them), the plot could take one of two turns: either she'll secretly lead Kowalski on over the course of the episode and try to squeeze as much valuable info/tech out of him as possible, or she'll reveal her allegiance at beginning and attempt to bribe Kowalski over to the dark side. As an earlier WMG points out, Dr. Blowhole is more Kowalski's nemesis than Skipper's, by virtue of his complete freedom to do or make whatever he wants For Science, and Kowalski is already jealous of that. If it suddenly reaches the point where making a Face Heel Turn means not only getting unlimited scientific freedom, but also getting the girl...
 * Alternately, at least Skipper and maybe the other penguins found out the truth, but Kowalski didn't. Skipper may have decided that there's little to no danger of Doris coming back, and so he chose not to break Kowalski's heart by telling him. ("She just wants to be friends with you" is bad enough, "She just wants to use you for her boss's evil plots" is even worse.) Under that interpretation, maybe Skipper's suspicious "No Doris, Kowalski must never know" dream was actually him asking dream-Doris not to tell dream-Kowalski that she's an evil agent out to break his heart. (Dreams. They rarely make sense.)

Of course, whichever way the plot goes, by the end Kowalski will choose the penguins over Doris. Attempting to bring Doris to the side of good as well is optional.

Fred the Squirrel really is the Red Squirrel.
It went Just As Planned. First, he was Obfuscating Stupidity in order to win the trust of the penguins (especially Private). Then, he manipulated them into finding Buck Rockgut's hideout. Then, he dressed up as the Red Squirrel in order to carry out the final phase of his plan, finally sending Rockgut away to nowhere. You don't believe it? Then you have to learn to think more like Rockgut. Do you know who also doesn't believe it? THE RED SQUIRREL!

The Penguins will eventually get their very own cinema movie.
Because that would be awesome.
 * It's actually been confirmed that a movie based on the series is in the works, under the same team that created Megamind. In other words, it's destined to be a blast!

Buck Rockgut is a Take That not only on paranoia in general, but also specifically on Cold War anti-communist paranoia.
Come on, the Red Squirrel? Also, I don't know about the English original, but in the German dub, the Red Squirrel has a slightly Russian accent.
 * Seconded. More specifically, the episode can be compared to McCarthy's Communist "witch-hunt" trials, with Rockgut representing Joseph McCarthy. (And the Red Squirrel's also got an accent in English.)
 * In "A Visit from Uncle Nigel" he even says "Do svidania" at some point. As for me, he is quite blatant allegory to the Red Scare, even in the name.

More than one of the penguins is biologically female.
Would reduce the Unfortunate Implications mentioned above, and the whole Monstrous Regiment potential is fun. The way with the fewest Unfortunate Implications and/or the most potential for humour would probably be if all of them except Private, who fills The Chick role, were female.

Central Park Zoo is classed by the penguins (and other animals) as a prison.
Most really good parks nowadays have wide open spaces. Take San Diego zoo, or Disney's Animal Kingdom in Florida. Huge, simulated natrual habitats - designed to fool even the animals there that they are really in the wild. Look at Central Park zoo - small enclosures, constant supervision, and many of the animals are violent or have massive mental problems. And a large number of them are always trying to get out.
 * Maybe, but it's still better than Hoboken.
 * Alternate version of this theory: it's a sexuality correction camp. Since so many of the critters are of endangered species, it's important that any tendencies towards homosexuality and/or cross-species attraction are removed. Going by the amount of Ho Yay and the many examples of the Cargo Ship depicted on the show, it's not working very well.

Joey is actually a girl.
It's suggested above that he could be FTM, but it's also possible he's actually a ciswoman with an unusually masculine voice. The only other marsupials in the zoo are the koalas, who are never awake when Joey is so she doesn't get to talk to them much, and the others aren't familiar enough with marsupial anatomy to know that only females have pouches. The reason "he's" constantly angry is because she's constantly being mistaken for male to the point that she's given up correcting everyone.

Fred's never-seen grandmother is the Red Squirrel.
All we know about Fred's grandmother is that she is not the crazy old squirrel hag in "The Lost Treasure of the Golden Squirrel". Rockgut described the Squirrel as "he", but considering both Rockgut's sanity level and the number of other characters on the show who could potentially be of a different biological sex than they present as (see above) ...

The fact that there are no Wild Mass Guessings on the episode "It's About Time" so far is the final and ultimate proof that the reality of quantum physics cannot be understood by human brains.
Seriously, this episode screams for Wild Mass Guessings, but there are none so far.

The show isn't, in fact, an alternate universe; Private's promotion in "Concrete Jungle Survival" followed the same line of continuity.
The episode occurred before Madgascar, and is a prequel to the entire show and movie story line. Private wanted to be promoted desperately before the trip to Madagascar, so the penguins sent him through that tedious adventure. Why are the lemurs there? Private was lonely, so his confused and exhausted imagination made up three companions for him to be with.
 * Alternate theory: The show takes place after the second movie. After the honeymoon, the Penguins and the Chimps returned to the zoo or were brought back. After hearing about NYC so much, King Julien, Maurice and Mort shipped themselves there. And the others remained in Africa/Madagascar.

Private is a fan of Princess Luna.
Moon Unicorns, anyone?
 * Private is a "Brony".

Rockgut and the Red Squirrel are a parody of the "Red Scare".
Rockgut represents America's obsession during the second Red Scare about the infiltration of America by communist spies which is why he accuses everyone of being the Red Squirrel (Communist spy), the Red Squirrel represents Communism as itself. Both are shown as either crazy (Rockgut) or incompetent (the Red Squirrel doesn't seem to do anything at all) which represents the way communism and Patriotism (in the extreme form) are seen nowadays: Communism has proven itself as insufficient and the extreme Patriotism is regarded as risible. Also both are obsolete.
 * Or, its meaning is that communists in general (Red Squirrel) didn't really do as much to America as the Rockguts of this world would like to believe...

Hoboken Zoo is going to be a force to be reckoned with
All the villains so far in the show have been sent to Hoboken. Maybe Dr. Blowhole is planning his HQ and is going to have a group of Psycho Rangers to help him kill the Penguins?
 * Confirmed, but not in the way you think...

Buck Rotgut, Nigel, and the Red Squirrel have a very complicated backstory that goes much deeper than "good vs. evil".
Okay, so once upon a time the Red Squirrel was a real player and a two-timing jerk. He decided to date both Nigel and Buck, however they found out and, in tears, both dumped him.The real reason they were hunting the Red Squirrel was that they wanted to confess their feelings. Despite the tragedy, they still loved him, and were determined to find him again. Red, however, felt terribly guilty, and certain they would try to find him and give him a beat-down, he fled the town and hid far away. The acorn thing was just a distraction, to try and fool anyone who questioned his reasons. And when Nigel found him, he was too scared to put himself out there, especially with so many people watching, that he forced himself to act like they had no backstory and were only nemeses.

The penguins are really under Kowalski's control, and the whole thing is just an experiment he's overseeing.
They were first used in a scientific experiment to make them moer survivable, and smart. 1. Of course the prototype was Rico but the compounds they infused him with didn't make him smart enough but instead he had an excess of testosterone making him human equivalent of manly. 2. Next was private, but in response to Rico's problem they set the testosterone too low, and got, well... 3. Then was Skipper, so close they were. He was well adjusted, great memory, intelligent enough, and had good leadership qualitys, but they wanted more. 4. Finally their greatest acheivement, Kowalski. He showed signs of intelligence that rivaled some human minds, he was a good order taker, and showed excellent leadership qualities. The original testers were all ready to assimilate the prototypes, when Kowalski wrote, in english, on paper, that the four of them looked like the perfect cover, for the perfect Spy Team, with Skipper, the gruff one, as acting leader, until further notice.

The whole show is a hallucination by one of the penguins.
In reality, whichever penguin is doing the hallucinating is a human in a mental hospital. To cope with his horrible surroundings, he retreated into an elaborate fantasy in which all the inmates are zoo animals, and he's able to participate in exciting adventures, help others, and feel like he's doing something to escape. Their adventures are all metaphorical variations on his real escape attempts. And now I want fanfic.
 * Now that's clever, but when does the main penguin get lobotomized.
 * Cruel people would suggest that, if it's Rico or possibly Private, he already has been.
 * Speaking of fanfic.

Julien is perpetually stoned off his head.
Lemurs have in fact been known to get high from centipede poison; they don't actually eat the centipedes, just lick them. So if the zoo has a bug exhibit ... gotta admit it would explain a lot.

The penguins were there to witness the events of 9/11.
Disturbing as this theory may be, it's horrifyingly easy to imagine Skipper convincing the others that it was their duty to defend their hometown of NYC. They were too late.
 * King Julien was so outraged when he learned about the attacks that he calls to the sky spirits to punish the terrorists.
 * A sky spirit killed Osama Bin Laden? I knew it.

When Dr. Blowhole returns again, he'll be even worse than before
His motivation for his plans was revenge on humanity for using him as a show dolphin, especially the ring of fire trick. Skipper put him back in that situation and eventually, his memories will probably return like Skippers did. Just how do you think he'll react to his archenemy putting him back in the same situation that drove him to evil?

Skipper is a 'Sky Spirit' so to Speak
That's why he is older then should be physically possible for a penguin (he implied he fought in WWII), why Manfredi and Johnson seem to have died so often (he brought them back to life numerous times until people started to question their immortality), why he and his team can survive things that would kill normal animals (Skipper himself spends hours at the ), and explains all the times spirt guide Alex interacted with him and the world, like driving a car and lifting him. He forgot he needed to hide his powers.
 * to add to that theory, let's look at when Julien has sincere interactions with his Sky Spirits... Skipper is usually involved. Julien's doing a raindance to stop a drought? Skipper seeds the clouds with salt. Zoo is freezing cold? Skipper turns on the heat. Julien offers to help the sky spirits in return? Skipper sends him a radio because he needs help. Julien misses the thunderbolt? A Cloudburst happens. I'm sure there are other times too.

Manfredi and Johnson and the Solider and Demoman from Team Fortress 2
hence why every time he tells the story it's different, the re-spawn technology make sure they keep coming back to life after dieing in X way. as for why the solider and demo? the Solider is practically Skipper in man form, and Demo is Rico only less insane and more alcoholic.