Drake and Josh/WMG

Megan is a genetically engineered prototype for Azula from Avatar: The Last Airbender who was banished to our world when it was discovered she couldn't firebend.
They also forgot to make the early version cool, which is why she's a Creator's Pet.

Megan is the child of Satan and a Mary Sue
This explains everything.
 * Bella had a child with Satan..?
 * She doesn't have issues with vampires...
 * Maybe she thinks they sparkle?
 * Maybe the idea of Edward as a God is just a ploy from Stephenie Meyer to make us forget he's Satan.
 * So, Megan is banged by a pedophile werewolf?
 * ^ Sounds good to me!

Megan is a Kira in training
Think about it. Everything goes EXACTLY as planned for her. There is no way she can grow into teenage years and adulthood without becoming a Kira.
 * This actually makes sense. I remember in one episode where Drake and Josh accidentally kill Megan's hamster, but strangely, decides to not get revenge. This almost literally drives both Drake and Josh insane due to them both thinking that the other could be involved in a Xanatos Gambit orchestrated by Megan. This eventually culminates in the floor of their room breaking down underneath them, dropping them into the garage. Megan looks down and says "I didn't need to get my own revenge. You two boobs did it for me." Drake and Josh then mumble that "she got us...without getting us." Just to rub salt into their wounds, Megan then brings out her (obviously alive) hamster, saying that he just kinda fainted.
 * No. She is Eragon in training. Don't be ridiculous.

Megan is the Ultra Humanite's latest body.
Hey, he was once in the body of a giant gorilla. Why not a little girl?

Josh's entire life is a Truman Show Plot... and Kristoff hates him
Sure, Truman's Kristoff was weird, but he tried to provide Truman a nice life. Josh gets tormented by his suave sibling, that weird evil little girl, his boss, the POLICE, and random MOBS OF PEOPLE IN THE STREET (see 'Theatre Thug' for the last two).

Megan is Haruhi or a mischievous god)
Coming to think about it... Nothing goes wrong with her; and she never, ever gets bored. Otherwise, our world would be destroyed. It could also explain Drake's and Josh's lack of luck - they might be her personal puppets.
 * She's not Haruhi. Haruhi can be thoughtless and cruel at times, but she has a nice side as well. It's a different reality-warping mischievous god.

Megan is from 511 Kinderheim
That's right, she's a survivor of the program to produce a new Hitler. Why doesn't she speak with a German accent? Why doesn't Johan?
 * If she wasn't raised German (or around people with a German accent), then she wouldn't have a German accent. Simple as that.

Drake and Josh were Omnicidal Maniacs in a former life, and Megan is their karmic punishment
There is no other reason that they could deserve.... this.... * cringe*

Megan is a plot by the creators to make a character they can kill off without anyone feeling bad
Think about it, and it becomes clear. They just haven't gotten to the episode titled "Megan Dies....horribly!" If they pull it off correctly, only time will tell. Here are a few reasons.
 * She's female, and thus less likely to be Draco in Leather Pants.
 * She's a Creator's Pet.
 * She's pure evil without being cool.
 * She deserves to be punished, and karma is... anyway...

Drake will die from AIDS

 * Why? Is it because he's a man-slut? Will Megan finally cross the Moral Event Horizon and deliberately infect him with HIV? Help us out here!
 * It's too late for her to cross that, she already did when she tortured Drake and Josh psychologically

After Drake got famous, he landed a spot on The Amanda Show and later convinced the execs to bring Josh into the fold.
Most of Josh's sketches were with Drake because Josh was nervous about being on TV and Drake didn't want him to get kicked off. Performing with Drake was easier for Josh because the two have natural chemistry.

Carly from ICarly is Megan in disguise.
After a "prank" goes too far, Megan accidentally kills Drake and Josh, leading to her fleeing San Diego for Seattle. She has Crazy Steve drive the getaway car. They create false identities for themselves in Seattle: Megan becomes Carly, and Crazy Steve becomes Spencer.

Carly and Sam were friends when Carly was Megan because of their complementary personalities and because Sam supplied non-lethal weapons to Megan. This is why Megan went to Seattle -- she would have someone to vouch for her. The massive amounts of Les Yay between Carly and Sam are due to Megan/Carly's Heel Face Turn, which she only did to avoid raising suspicion. She didn't realize this would turn Sam on.
 * Who, then, is their supposed father? And why is she okay with appearing all over the internet?
 * In memoriam to Drake, Sam keeps his picture on her locker door.
 * And then, Drake appeared as a ghost in iBloop.
 * Do you really think that Crazy Steve could pretend to be as normal as Spencer?
 * Maybe he's on meds?

The Zeke and Luther universe is an alternate universe to the one in Drake & Josh.
Most of the characters are major Expys. Luther to Drake. Zeke to Josh. Ginger to Megan.
 * It'd have to be a Bizarro Universe because Ginger is at least somewhat likable, doesn't get away with her schemes half the time, and sometimes has a perfectly justifiable reason for being mean to the title characters.
 * Alternately, Zeke and Luther is a Spiritual Successor or even a sequel to Drake and Josh. Given how the title characters aren't perfect expies of each other, it's possible that Zeke and Luther are descended from Drake and Josh.

Megan buys her equipment from the same place that Freddie from ICarly buys his. Acme Products.
Acme Products in this case being some kind of dodgy black or grey market importing from China, Hong Kong, Japan or Taiwan. How else could a pre-teen and a 13 year old afford all that equipment?

Megan is a malevolent trickster Time Lord
Yes, yes, this is admittedly a TERRIBLY overdone WMG, but surely this troper can't be the only one who thought, "TARDIS!?" when Drake and Josh discover an entire secret room next to her own full of high-tech tracking devices (used to keep watch of Drake and Josh, naturally) and other gadgets, and Meagan somehow makes it all disappear before the pair can show it to their parents.

Megan's bitchiness is all Drake's fault.
She was once a sweet kid that would often got bullied everyday. Drake often gets fed up with this and starts to train Megan into doing pranks. However, this goes too far. Way to go, Drake.

Megan started her evil buisness at the age of years 1-3, leading her to do more evil!
In "Foam Finger", it was revealed that Megan threw a cookie, causing Drake and Josh to fight (Long Story). She likes how she did trouble and got away with it. This was done time after time causing her to get clinged onto it, causing trouble, never getting in trouble, ect. She than decides that she herself only, no-one else will make her 2 brothers life a living hell. However, she LOSES HER STANDARDS WHEN SHE LETS HER BROTHERS OUT FOR DEAD ON A HELICOPTER WITH NO FUEL! And what was her first response when she saw them alive. "Did you bring any tuna?" Now when she does this in the real world to other people, she will go too far and do this to the police, sending her to execution. The parents will hear about this, relieze Drake And Josh were right, repay them and live happily ever after.

Megan's the reason the kids aren't taken away from the parents because they're bad at parenting.
She knows that no other morons would let her get away with the stuff she does so she somehow got child services to stay away. There are two options to how. 1) Threats. 2) She said some equipment she had was government issue, so she has connections with the government and can simply tell them to stay away.

Megan took Drake and Josh's shenanigans and turned them into a TV show.
In Victorious, the gang talks about Drake and Josh as a TV show. However, Josh could be seen as a background character in an earlier episode. Why is this? Because Drake and Josh are real people in their world, but they are also TV show characters thanks to Megan. We once saw her watching Drake and Josh argue through a hidden camera. She recorded everything she saw and turned it into a TV show without their knowledge.

Josh has multiple personality disorder, and Drake is all in his head.
Josh is constantly being blamed for everything Drake does because Josh is the one who's doing it. Any interaction anyone else has with Drake is invented by Josh. Either Drake is entirely in his head (the boy he wishes he could be), a boy at school he admires, or his step-brother who died. Picture this: It's the final moments of the series' finale. Drake and Josh are bantering in their room. You see their parents nervously listening at the door. The mother says, "He's talking to himself again." Walter replies, "I know. It's been getting worse." Mom agrees, "He just hasn't been the same since Drake died five years ago." Slowly pan off the parents and over to the hall table, upon which rests an old photo of Drake, smiling. Zoom in on his eyes. Fade to black.

You'll never watch it the same way.
 * A fanfic with almost that exact plot, but with the characters reversed can be found here: http://www.fanfiction.net/s/4341201/1/Always_the_Last_to_Know

Drake is Dib, Josh is Zim, Megan is Gaz
After an accident in Zim's lab, Zim, Dib. and Gaz's appearances are altered, and they get amnesia, Dib remembers that his name starts with a D, Gaz remebers there was a G in her name, and Zim, due to his alien mind, just forgets everything. This backs up my 'Jade is an Irken' theory, in a way.
 * In one episode Megan mentions a Pintendo 'GS' GS might as well mean gameslave, and Gameslaves might be made by Pintendo
 * Drake and Josh don't always get along, which could be a couple of memories that came back
 * Drake has a younger sister, at the series start . (And Megan has a G in it it, she could have just moved it to the middle of her name)