Chowder/WMG

The pilot episode is really the last episode.
Remember when Chowder and Panini have been mercilessly Flanderized? Well, that's because one can consider them to be the last episode in which there is a resolution to both Chowder's classification as a scatterbrain and the Will They or Won't They? of Panini X Chowder. Therefore, the so-called Flanderization of both characters were really intended from the beginning, and the pilot is just aired as the first episode, and takes place much later in the series.
 * My extension of that...

The Brain Grub episode is the first episode.
This episode acts as though the characters aren't aware of the fact that they aren't in a show. If we take this as the first episode, then all the other lampshade hangings and such make sense in every other episode.

Mung was the one that left Endive behind at her wedding.
It's been stated more than a few times over the course of the show that Mung loves the ladies (and continues to do so, even after being married to Truffles for god-knows how long.) It's also been stated that he hates doing things by the book. What started out as a possible full-fledged romance between him and Endive basically turned to rot after he found that he couldn't stand her textbook-perfect nature; that, coupled with the fear of giving up his bachelor lifestyle, caused him to get cold feet and run off on his own until he met Truffles, who didn't give a crap about how he worked or who he flirted with on the side.

Also, before anyone mentions the "Mung and Truffles have been married for 450 years!" bit, keep in mind that Endive's age isn't even hinted at yet, meaning that she could be as old as he is...
 * The latest Chowder episode, Schnitzel Quits! seems to be building upon this.
 * On that note... perhaps along with Mung's womanizing tenancies, Endive slowly became crazy, fearing that she might loose Mung, and scared the crap out of him. So he ran off and fell for Truffles, who was considerably more attractive and far less sour back then.
 * Alternately, they were arranged to be married, but something caused it to fall through. In a recent episode, when Mung explains to Chowder what an arranged marriage is, he says something along the lines of your parents forcing you to marry a crazy woman instead of marrying the crazy woman of your choice. Oddly specific for a definition.

The entire series is All Just a Dream, a dream induced by Chowder getting food poisoning.
Because that would explain the Negative Continuity, the bizarre colors, people, and cars, the surrealness of the episode plots, and Chowder's obsession with eating.
 * If this is the way you see it, maybe you should stay away from shows like H.R. Pufnstuf, Gimmie Gimmie Octopus and Anpanman too.
 * You forgot to add Anime to that list.

gazpacho is secretly a pirate.
that's why he hates ninjas

Alternatively, the whole series is the hallucination of a mental patient.
You said it. The entire city is extremely surreal, and nothing seems to logically make sense.
 * That would explain the freaky dancing pig thing.

Before entering puberty, the species which Chowder and Panini belong to are in a state of...what's a nice way to put this....

 * ...a state of being mentally challenged.
 * Either that, or Chowder is simply in an extreme state of mental disability. I mean, seriously, in the episode Brain Grub, he failed to comprehend the challenging concept that spoons belong in the spoon drawer. In case you fail to get that, he shoved a spoon into a watermelon, nearly shoved a spoon in an electrical socket and actually shoved a spoon up Schnitzel's ass before Mung just gave up and did it himself. It's the greatest case that he's mentally challenged, but certainly not the only case.
 * And while we're at it, Panini isn't exactly the sharpest knife in the drawer, either.
 * Alternatively, it could just be a side-effect of Chowder being really, really hyper (he does eat sweets constantly to the point where it can only be concluded that his species does not get diabetes). He might be suffering from ADHD as well.
 * The preview for the upcoming episode seems to highly suggest that Chowder is indeed simply suffering from a severe state of hyperactive attention deficit disorder.
 * Well, to be fair, Truffles likes to hit people in the head with a frying pan a lot, so maybe Chowder had one too many bonks to the brain.
 * Word of God says Chowder and Panini are cat/bear/rabbit hybrids.
 * Supported by Mung telling Chowder to be a great chef all you need is a great mustache, therefore he needs to hit puberty to be a great chef.

Alternatively, the species Chowder and Panini belong to are of the tanuki.

 * Because I don't really buy the whole "cat-bear-rabbit thing" idea, Word of God or not. Notice how both of their tails are raccoon-shaped and even striped, with ears always perked up. It could just be a coincidence that the female species happens to have bigger ears and can be more rabbit-like. Along with this, in traditional folklore of a tanuki, they're "reputed to be mischievous and jolly, a master of disguise and shapeshifting, but somewhat gullible and absent-minded." Perhaps not so much the middle, but are rather jolly a lot of the time, no? Gullible and absent-minded might be more prominent in the males, though. And because this is a children cartoon, this variation of the species have no huge testicles.

Chowder is the true idealized form of Instrumentality

 * Yes, you read that right. Not just another crazy Evangelion theory, but one that says that Chowder is the universe Shinji ultimately wishes for. Wishing to be able to live in the most innocent universe he can imagine, Shinji reformatted the entire universe into that of a children's cartoon, where he's the cute, cuddly and naive star. To him, everything is perfect - no need to defend humanity or prove his manhood, just live carefree as a young apprentice chef. Because it quite literally is a cartoon, the continued existence of the universe depends on Shinji's/Chowder's continued ignornace, which explains, well, Chowder's severe ignorance. The episode "Brain Grub" shows us what happens when he becomes intelligent; he realizes he's in a cartoon, and the universe begins to collapse on itself. Only by becoming stupid again is the universe able to persist.
 * Alternatively, Shinji is the "King of All Cosmos" (see Katamari Damacy theory below)
 * Where does Gorgonzola fit in all this?
 * Simple. 'He's' Auska. They do have similar personalities! Obviously, Shinji/Chowder is trying to blot out the hurtful reality he left behind as much as possible, but he put Gorgonzola/Auska there so he could have a counterpart in this universe. Remember the School Comedy reality he thought of in episode TV 26? Of course, this also means there are counterparts of Rei, Gendo, Misato, as well. Any seggestions?
 * Sure. Gendo is Mung Daal.
 * Guess that must mean Rei gets to be Panini, and Endive would be Ritsuko...which would leave Misato to be Truffles. Or maybe vice-versa, but it's hardly a perfect fit either way. At least I see Kaji being a fit for Gazpacho. For being the one who came up with this theory, I sure didn't think it through all the way, didn't I?
 * Rei and Panini are nothing alike, unless you're taking Rei's characterization from the Angelic Days manga... then it would make marginally more sense. An AU of an AU, why not?
 * This would be Shinji's view of all the characters in this state of mind. So maybe this is how he wish Rei was.
 * So near the end of "Brain Grub", instrumentality was starting to collapse and give way to reality again, until Shinji made the choice to erase his growing self-awareness and immerse himself and the rest of humanity back into the carefree life of Marzipan City. That makes a scary amount of sense...

Marzipan City really is made out of marzipan.
Because if you can mold it into tiny little intricate shapes, then heck, why not an entire city where almost everything revolves around food?
 * This conveniently explains why everything is edible, and why Chowder pretty much eats everything without adverse consequences.

Chowder's Cute Little Fang is the same as his "Wisdom Tooth"

 * As seen in "The Puckleberry Overlords." Yes, the Wisdom Tooth doesn't look like a fang (or cute) at all, but then neither do any of his teeth when viewing them from inside his mouth.

Chowder takes place in the same universe as Katamari Damacy

 * Almost confirmed by Word of God no less; the being in the sky who wears purple pants is The King of All Cosmos.
 * Not to mention this very funny sequence from Grubble Gum. Complete with parody Katamari theme!

Schnitzel is actually a Pokémon.

 * The species name is Radda, and Schnitzel is just that particular Radda's nickname.
 * Since Endive fell in love with Schnitzel, does this mean she's into bestiality?
 * Yes, even if he isn't a Pokémon.
 * Also explains being referred to as a Rock Monster, and trying to solve most problems by throwing rocks.
 * Jossed. Rock monsters only speak like this when under stress. When allowed to relax, they can speak coherently. Schnitzel is just always stressed.
 * I don't think that time he talked was canon.
 * Is ANYTHING in Chowder really canon, ever?

Chowder is Light Yagami

 * This is the world he desired, a world full of honest hardworking people. There was that one guy with the plunger, but he was pretty stupid anyway. Plus, when Chowder made his hand really big, it was all in a misguided attempt to help.
 * Paninni is Misa...we all know that. Gorganzola might be L.
 * Then Ceviche is probably Matsuda. Wow, this fits better than it should.
 * Schnitzel is totally Aizawa.
 * Marmalade might be Takada

Marzipan City is built upon Candied Island
When Knuckles and Flapjack finally find it, Flapjack and Chowder will start the eating contest to end all eating contests!
 * Chowder will win.
 * No, Flapjack.
 * But, Flapjack isn't much of an eater, right?
 * K'nuckles doesn't usually feed him, no.
 * No, it'll be K'nuckles. What, it would be hilarious!
 * Alternatively: K'nuckles eats all the food. Then Chowder eats K'nuckles for the win.

Chowder's world is the fairytale world in the far future
Our time to be exact. It's a different world or universe or whatever but it does make sense. Mung is probably an elf and Endive an ogre. It also explains why there are cat/bear/rabbit hybrids. If there are half humans in fairy tales, then why not hybrids of other things?

Male rock monsters are rumored to be very well equipped
This is why so many elderly Marzipan City ladies are hitting on Schnitzel (no, it's not just Endive - See "The Big Hat Biddies""). The reason why Schnitzel took a job where he always gets stuck with all the menial labor, is that his only other option was to become a gigolo, and that was beneath his dignity.
 * ...Schnitzel has dignity?

Chowder has Asperger's Syndrome or some form of autism
It would explain his tendency to blurt out random things without thinking about what he's saying, and his social awkwardness. In an early episode it is also implied that he's dyslexic, which is a common symptom of autism.

The theme song is an in-universe commercial for Mung's restaurant
This might be a pretty obvious WMG, but the song's all about cooking and food, the lyrics are sung by Mung and the gang as an invitation for people to "stay awhile 'cause something's always cooking", and it ends with the characters chattering to each other about how well they thought the song went. It gives the impression that the theme song's really an in-universe commercial they're putting together for the catering company.
 * So true it's probably canon. That also explains why Schnitzel hated hearing it.

Chowder is a girl
No one else knows, and Chowder doesn't realize they don't know. That's why (s)he's horrified at Panini's advances and why (s)he frequently enjoys wearing girl's clothing. This is also why (s)he never hooked up with Marmalade, despite being very compatible with her...not to mention the whole purple clothes thing.


 * If that is true, then once one realizes how much Fan Disservice we've been given of Chowder.... Oh God, NO!
 * Nevermind that Chowder spent half the episode "Kid Schnitzel"  mostly naked!
 * The series finale . His status as a male is pretty much confirmed.
 * Sex change! There was a sex change!

Marmalade is the child of Kermit and Piggy
Gazpacho did call her a "Pig Frog Girl"

Marzipan City is hell, or at least in hell.
Everyone in the city committed one of the Seven Deadly Sins, and for their punishment have been warped into bizarre, animal-like forms, had their sins exaggerated to the point of absurdity, and put into an illogical city that sometimes seems to be actively trying to hurt them.
 * Chowder was guilty of gluttony; Ceviche and Panini both were guilty of lust (and as part of their punishment are now infatuated with people who don't care for them); Truffles, Endive, and Rosemary were guilty of wrath; Mung Daal, Marmalade, and Peanut were guilty of pride; Gazpacho was guilty of sloth; and Schnitzel wasn't guilty of any of the big seven, but he did repeatedly break the commandment about not taking the Lord's name in vain, and that's why he's been cursed with only being able to say 'radda.'
 * IT MAKES TOO MUCH SENSE!
 * I know this show pretty well and I don't know anyone named "Peanut". I mean I really don't think there is anyone by that name. On another note, I think pride suits Endive more considering how perfect of a chef she thinks she is. She really doesn't get that mad. Don't forget Gorgonzola, who committed wrath.

The original Schnitzel died in the episode "Chowder's Catering Company" and was replaced by Schnitzy, his twin.
At the end of Chowder's Catering Company, Schnitzel jumps in a barrel and rolls into the Wonderhole in which, according to Chowder, nobody can ever get out of. He was replaced by Schnitzy, his exact twin, who performed at the comedy club Gazpacho also peformed at in "Gazpacho Stands Up". However, Mung and Chowder fail to beleive that original Schnitzel is still trapped in the pit.
 * The ending of "Dinner Theater" shows that Shnitzel is played by his identical twin Shwitzel, so it's likely that Schnitzy and Shwitzel are both the same person.

Chowder has an eating disorder
Why else would Chowder eat EVERYTHING and ANYTHING he comes into contact with (occasionally residents of Marzipan City)?
 * What was your first clue?

The world of Chowder will be completely overrun by
They will not be able to keep that whole agreement in the the finale and will keep on

Chowder is a distant relative of Eek! The Cat
Just compare the two. Although probably not immediate family (Chowder being a hybrid creature), the two do bare more than a passing resemblence to each other.

Gazpacho's mother was dead.
Gazpacho's tendencies on always saying "mother always says" is a mean to cope of her loss.

Chowder takes place in the same world as Toriko
Both Marzipan City and the whole world of Toriko are food obsessed, and the quality of food is directly dependent on how hard it is to obtain the ingredients and prepare them into an edible form.

Ceviche is biologically female
A kid FtM.

Chowder's parents are around.
In the episode "The Deadly Maze", during Gumbo's flashback of when he quit being Mung's apprentice, Mung says "Well, we lost another one. Shintzel, get the apprentice catalog!"

So in Chowder's world, or at least Marzipan City, its common for kids to be send off to the apprentice delivery. Chowder's parents were poor and want their son to have a better life. They have him put among the other chef apprentices since he likes food, a lot. Off-screen, Chowder writes to his parents about his many adventures.