Ratatouille/WMG

The movie was created in order to defuse a common insult against the Disney Corporation.
A popular slang term for Disney is "the Mouse," after their most successful intellectual property, Mickey Mouse. Detractors like to spin that into "the Rat," invoking the animal's reputation for being sneaky and ridden with disease. Hence, Disney commissions Pixar to make a film about a lovable, soulful, artistic genius of a rat in order to improve the species' public image and make "the Rat" into a compliment.

The movie was created as a wake-up call for Disney.
The folks at Pixar have often stated their love for classic Disney films. And just about every other critic noticed there was something familiar about the concept of the film: after a beloved chef's death, a new head chef capitalizes on the reputation of said chef by using it to churn out inferior frozen, prepackaged foods.

The movie was intended as a Take That at Disney.
Ratatouille was developed while Pixar and Disney were trying (and failing) to reach a new profit-sharing and distribution deal. If Disney and Pixar had not reached a new agreement, Ratatouille would've been Pixar's first non-Disney movie. Puts the scenes of everyone repulsed at rats in a new light.

That's no hallucination; that's Gusteau's ghost.
Think about it -- who is the real winner here? Gusteau's son attains his birthright and Gusteau's restaurant regains its reputation. The greedy little twerp who had pimped out Gusteau's image is ruined. All because Remy, the world's greatest chef, had a "hallucination" which guided him to the restaurant and encouraged him to help Linguini out. Maybe it was a more active form of guidance than Remy thought; Gusteau just went along with the "figment of your imagination" idea because he figured Remy would be more likely to accept a vision brought on by intense hunger than a departed spirit.
 * But Gusteau's restaurant is forcibly shut down at the end!
 * There was no choice. Gusteau wanted to restore his restaurant's reputation and punish the fella who wrecked it at the same time, but that fella was the only person who could undo the damage. Something had to give. Besides, the restaurant's spirit lives on in a new, lower-profile form.
 * This is canon. Gusteau leads Remy to his restaurant. Remy can't have hallucinated that, since there's no way he could have known where Gusteau's restaurant was.
 * Not necessarily. He found Gusteau's restaurant, he didn't look for it.
 * Gusteau didn't know he had a son even when he was alive -- the mother told no one -- so that could be the real Gusteau just claiming to be a hallucination in that scene.
 * Near the end of the movie, the last words of Gusteau to Remy indicate he was real. So does his touching Remy -- hallucinations normally can't do that.

Gusteau is real, but doesn't guide Remy to his restaurant with the hope to save it.
He wants to help Remy discover himself.

Gusteau actually cooks as bad as Linguini: he also had a rat in his head
Eventually Gusteau became independent and took the popularity to himself after learning on how to cook from a rat.

Remy is Gusteau.
Think about it. Rats don't live long. Remy is young for a rat, and so he is only a few months old at the most. He certainly wouldn't have been born until after Gusteau died. By simple irony, Gusteau was reincarnated as a rat; but his previous life was so vivid that he was still a food-lover. The ghost-Gusteau that Remy keeps seeing is his subconscious broken memories of his old life. This is why he is so attracted to Linguini. He wants to.
 * This WMG makes the movie 10 times better.
 * Or it could be a type of Fridge Horror especially if Linguini were to figure it out

Ego is Gusteau.
Suffering from a continual inferiority complex, the man created an entirely alternate personality to be his exact opposite and criticise his every move. He's stereotypically French? His opposite, stereotypically English. He's grossly overweight? His opposite, vampirically thin. He even goes so far as to give the man a name implying an origin in the recesses of the unconscious mind. Ultimately, he grew bored of cooking; using some money from an old nest egg, he underwent dramatic surgery to bring 'Ego' - previously played by an actor - to life, until the time came to test his beloved long-lost son. This adds credence to Remy's cooking - it's so good that it inspires memories in a fake personality who logically shouldn't have them.
 * Minor comment about the name: the ego is the only conscious part of the mind. On the other hand, criticizing the ego is what the superego does.

Colette lies about the kitchen crew to inspire or spook Linguini.
So does the sous chef. Surely he didn't single-handedly create the hole in the ozone layer.
 * Doesn't work; one of Horst's stories is that he killed a man with his right thumb alone, and he later threatens Skinner with that thumb after the restaurant changes to Linguini's ownership. The threat would be meaningless if Colette was lying about his past.
 * It leaves the stories of everyone else open, though.

The movie is part of the The Hitchhikers Guide to The Galaxy continuity.
Remy is one of the smarter-than-human mice projection of the alien race that created Deep Thought. He just lost interest in the research of the ultimate question to Life, the Universe and Everything, in favor of cooking. The ability to control Linguini by pulling his hairs is not an anomaly; it's a feature of all humans.
 * Man, that program's been running so long that some of the original mice have evolved into rats!

Remy's colony is descended from the Rats of NIMH.
In an effort to escape NIMH for good, the colony left their valley and traveled to France, eventually giving rise to a colony of rats that were smart enough to build boats, develop language, read, cook, etc.
 * No, wrong branch. Remember Jenner? He moved to the city for easier access to human resources. He and his followers were much more successful than Nicodemus and co. thought, and now their descendants have spread as far as Paris...
 * That's based on book Rats. If working from the movie, then include The Secret of NIMH 2 in continuity; that puts Thorn Valley in commuting distance to one city and not insanely far from a second. It would be a simple matter for part of the colony to leave the valley for the sewers with relatively few repercussions. (Or leave NIMH itself if there are Rats there.) The generations after can spread as above.

Ego is a vampire.
Normal food holds no pleasure for him; eventually Linguini's dish is the only thing capable of inspiring enjoyment in him outside of blood.
 * It explains why his office is shaped like a coffin -- it's the place where he spends most of his time, writing reviews. He doesn't need to have an actual coffin because of it.
 * And it covers the fact why we see him only during evening/night.

Ego had an unhappy childhood.
The reason why he looks cold and dark-hearted and his criticism is direct and sharp is because he wants to impose his childhood misery upon others. It is also the reason why the ratatouille inspired enjoyment in him: he was reminded of his mother, who could possibly be the only person who cared for him.
 * In connection with this WMG, I've always believed that not only was Ego's mother the only one who loved him, but that she probably died when he was very young. Also, since the flashback begins with young Ego standing in the doorway trying not to cry, I get the feeling he was bullied a lot, which could also explain his sharp criticism as misplaced vengeance on his childhood tormentors. One way or the other, I think we can safely assume that something very traumatic happened to him at some point.
 * No, he was crying because he was hurt. Notice the crumpled bicycle in the background, and how Ego's knees are bloody.
 * This WMG could still work. How do we know it was an accident?

Linguini is the hapless farmer from "Lifted."
That farmer was slammed around his farmhouse like a pinball by that goofy alien. Repeated head trauma would explain why Linguini was so bad on his feet and unable to hold down a job. Living in the US would explain his American accented French, and why Gusteau did not know of him before his death.

Ego is immortal.
He became so bored with immortality that he became a Caustic Critic, taking out his ennui on the food that he became bored with. The ratatouille brought him back to his childhood, when everything was still full of wonder, and he decides to be more constructive with his eternal life.

Horst suffers from Split Personality Disorder
That's why he always gives a different explanation when asked why he spent time in prison. Every single personality remembers it differently and that would also explain why most of the answers are so wacky: Great deal of those personalities don't have a 100% full grasp of reality and imagine something unbelievable, because they simply don't understand that it is possible. (I mean, robbing a bank with a ballpoint pen? Come on!) The reason Horst hasn't gone on medication is because he simply has no need for it: The personalities are just a little bit different and they share information and common memories so he can still cook efficiently no matter of which personality is in control. Why waste a lot of money and time into some unreliable pills and therapy, when he can just go on with his life and his coworkers only dismiss his quirk as a sign, that he doesn't want to reveal the 'actual reason'.
 * Actually, 'robbing a bank with only a ballpoint pen' could be a subtle reference to large scale embezzlement, fraud and fiddling of the expenses.

Horst is really Chuck Norris.
'Nuff said.
 * "I killed a man with this thumb." He just flexed that thumb's biceps.

Ratatouille is an obscure sequel to South Park: Bigger, Longer, and Uncut.
No no no, just hear me out; remember the chef who was in 'La Resistance', but never talks about it? That's really Mole; 'La Resistance' refers to the group of kids devoted to saving Terrence and Phillip, and the reason he never talks about it was because a) it's not exactly a noble resistance to talk about, and b) he was supposed to have died.

Renata Linguine was a Mafia Princess
She had to go back to her father after a long enough stint in Paris to fall in love with Gusteau and conceive Alfredo. Since Alfredo is half-French, he wouldn't qualify for membership in The Mafia and thus was left without the help of The Family when Renata died.

Ego's mom is the old lady from the beginning.
You know, the owner of the house infested by Remy's family. Hear me out: Ego's childhood home used to be in the country, this lady lives in the country. Plus, this lady must have been the same age as the critic's mother, since he's no rosebud either. Maybe Remy watched the old lady cooking, and got some of her style. Also, Ego might had been in a fight with his mother and cut the contact, making the scene where he tries the Ratatouille a lot more meaningful.
 * You know, This Troper likes this theory; when you consider that the woman just watched cooking shows all day it makes a weird sort of sense.

Skinner sabotaged Gusteau.
Skinner wanted to launch a line of frozen foods under Gusteau's name. When he refused, he purposely batched Anton ego's dish in order to loose a star. Skinner did not intend to kill Gusteau, only to dishearten him enough to let Skinner make the frozen dinners. Gusteau's death was a fortunate coincidence considering Skinner got all rights to his name and restaurant.

Ego's Childhood Flashback was just a metaphor.
Ratatouille wasn't Ego's favorite childhood food. It was a metaphor that Ego locked away his childhood along with his happiness and after eating Ratatouille released it.

The black and white report on Gusteau was a VHS
There are DNA tests and stuff.

Horst is The Joker.
Let's see, he has a Multiple Choice Past to be sure, but perhaps his "normal" appearance is just some good makeup. But wait you say, he's not a walking wasteland of Comedic Sociopathy right? Given how much of The Unfunny Horst happens to be, maybe he's trying to parody what he thinks normal people act like while on downtime. Even the Ace of Knaves needs a breather, after all.

Horst did time for public nudity and/or public urination.
And he's so embarrassed by it that he makes up crazy stories to cover it up and keep people too scared of him to really look into it.