Æon Flux. The TV show. Some episodes are worse than others, but the complete lack of continuity, bizarre dystopian setting, overtly philosophical conversations (or complete silence depending which season you're watching), and unusual symbolism that is indistinguishable from the Rule of Cool events. It's weird. It is, however, absolutely awesome.
The fact that the creator Peter Chung seems to actually know what's going on, but deliberately stops himself when he starts explaining it is either very annoying or very liberating depending on how you look at it.
None of this is helped by the fact that each episode is a self-contained story that is clearly already in progress, with no recap and zero exposition. That or a Jungian nightmare, take your pick, either one is both valid and complete bullshit.
The Grim Adventures of Billy & Mandy is more or less constructed from this trope. The various episodes follow vague premises with more Mind Screw moments and Big Lipped Alligator Moments than virtually any other show. A particularly memorable one though, is at the end of an episode where they unmask a villain (he's adult-sized) to reveal... an earthworm.
Parodied in Perfect Hair Forever: "I wish these hot dogs and cats were not symbolic of anything, and this was all just a dumb anime mindf*** !"
Transformers: Beast Machines was more of a Heavy Mind Petting, but it was still pretty clouded with symbolism, and the fact that it could be deciphered tended to raise another problem when the message didn't go over well.
The final episode of Teen Titans was really more of a No Ending, but it was such an over-the-top and inexplicable No Ending that it has to be mentioned here. It has been stated in interviews that the show's staff wasn't too keen on explaining things in the story; what transpired here can be best described as that policy's logical conclusion. Though, the sort of question Glen Murakami wasn't keen on answering were things about the characters' non-suited lives, and the "how did villain X get out of the Cardboard Prison last time?" These sort of things he considered unimportant, a distraction from the main plot. This was the only episode in which nothing was made sense of. (Well, Beast Boy does move on after the Terra incident - which we'd thought him over three seasons ago. The rest is pure randomness.)
The episode of Totally Spies!, "Deja Cruise". To make a long story short, it was like the girls' dreams were having dreams. The WOOHP contract may as well have this clause on it: "CAUTION: Prolonged employment at this occupation may cause you to lose the ability to differentiate between fantasy and reality."
Ed, Edd n Eddy: in "One Plus One Equals Ed", the titular trio try and know everything so they can become super-smart and famous. In their quest for knowledge, however, all of reality breaks down- trees are flat as cardboard, Eddy eats the sun, Nazz turns into a dinosaur, and on and on. The madness only ends when the Eds are flying on a balloon that gets popped by the animator's giant pencil. And they never speak of it again.
Eddy: (After three giant Kanker Sisters merge into a giant pair of lips) Ed, your story's getting weird.
Parodied in The Simpsons, where an advertising company produces a TV advert for Homer's plowing service, featuring a opera-singing woman screaming at a snow-globe before smashing it on the pavement. In black and white. The family's response sums it up well.
The "Mr. Sparkle" commercial from "In Marge We Trust", where a Japanese detergent mascot that looks like Homer Simpson's head shatters a two-headed cow like glass (among other things).
Similar to the ReBoot example above, "The Computer Wore Menace Shoes" only makes sense if you know it's a parody of The Prisoner.
The Futurama episode "The Sting", in which Leela's perception of reality becomes more and more deranged, with events that turn out to be dreams, a hallucination of a morbidly cheerful musical number, a 2001: A Space Odyssey parody, and descent into obsessive insanity. It turns out everything in the episode since the bee attack was her nightmare.
NC: I think my favorite episode is the one called “Future Tense,” where Goliath arrives in the future and all hell broke loose as Xanatos has apparently taken over. Trying to set things right, all the gargoyles get killed and slaughtered by Xanatos’ army. But then it turns out Xanatos is really a computer with all the memories of the original person. But THEN it turns out it wasn’t Xanatos at all; it was Lexington, who’s become overtaken by madness. BUT THEN it turns out it was all an illusion by Puck to try and get a mythical emblem from Goliath. AND THEN it turns out it may or may not have been a dream. AND THEN it turns out that Goliath is a woman! (A Photoshopped image of Goliath in drag appears with a dramatic music sting) Okay, that didn’t happen, but you get the idea.
At the end of the Super Mario World episode "The Yoshi Shuffle", Luigi's brain is apparently melted (giving rise to the Fan Nickname "Retard Luigi") following this exchange:
Luigi: Uh, did I catch the ball? Mario: Whaddaya mean, catch the ball? Youwerethe ball!
The Animatrix is an animated series inspired by The Matrix, but "half of it couldn't even be understood unless you were crazy or an art major."
The Canadian short La Salla. 15 seconds in, the main character is shooting replica cows at paintings for no obvious reason.
In Ugly Americans, the entire episode of "G. I. Twayne" is practically a giant Mind Screw episode towards both the main character Mark Lily as well as the viewers. As it turns out the entire thing is just a pre-enactment. This screws Mark so much he shows clear paranoia at the end of the episode.
To summarize, the denizens of Hell hold a yearly "pre-enactment" of the End of Days - that year, however, it looks like a Batman Gambit where they'd use the pre-enactment to start the actual End of Days. Hilarity Ensues.
Aang's stress-related hallucinations in Nightmares and Daydreams get so over the top that you might just forget that he's nervous about the invasion and start to think that the creators are on something.
Some Woody Woodpecker shorts can get very nonsensical, even by cartoon standards.
All of Adventure Time. Good luck trying to understand any of it! To sum up - there's a reason a popular Fan Theory is that the entire show takes place After the End.
At this point, the After the End status of the setting has been definitively confirmed.
Especially in "King Worm". It involves a dream sequence where there is a giant monster made of penguins, the setting randomly changing into physically impossible landscapes, and just about everything Finn thinks happens. Heck, even the title card looks surreal.
"Too Old". Mother-fucking "Too Old". The Lemon Kingdom plain does not make sense. When it ends with the Earl eating his brother, who crawls back out of his mouth one final time to free the subjects and urge the last normal Lemon to come back and dethrone the Earl, you're left wondering who slipped you the mescaline.
"A Glitch is a Glitch"? Well, it's also an inexplicable shift into 3D animation, where Finn and Jake defeat the glitch by copying a shock vid to make it throw up.
Regular Show, which usually starts out with a fairly simple, straightforward, and every-day plot (learning to play guitar, getting tickets to a concert, throwing a friend a surprise birthday party, etc), but by the last few minutes of the episode, their normal actions will usually have broken reality, woke up some kind of Eldritch Abomination, traveled through time, or they've ended up getting attacked by something. Usually something really messed up. And the really screwy thing is that after the cosmic horror part is solved, it's usually only an afterthought, at which point the characters focus on the normal subplot that got them into it.
My Little Pony: Newborn Cuties: Over Two Rainbows is the insane story of Rainbow Dash (before she had a rainbow mane) spending ten minutes whining about her scarf while Sweetie Belle is born (wearing a nappy)... via the crossing of two rainbows. As all this happens the ponies' mouths never move once. "What is this?!" is the standard reaction of everybody that tries to watch it.
Although it's a bit lighter than some of the other examples, the TRON: Uprising episode, "The Stranger". It mainly takes place in somewhere not-quite on the Grid, with a weird computer-like texture all over it, strange (for the show) colours, a villain constantly defying physics in an unsettling way even on the Grid, a bizarro doomsday device, and Beck nearly being boiled to death and seeing... Flynn-knows-what before he manages to break free. And to top it all off, it has an 'Or Is It?' ending.
The episode Dreamscapers of Gravity Falls. It features: a mind demon, a deer's teeth being pulled out of its mouth (and getting put back in), Dipper getting a gaping hole in the place of his stomach, some...interesting memories of Stan's (including him playing with his stomach and calling it Mr. Tummy), two technicolor anime boys, a giant rock in Stan's likeness, a very British English bulldog, Mabel getting her cuteness sucked away, kittens for fists, a question-mark-shaped beam coming from Soos's stomach, and the ending of the episode was Gideon breaking into the Mystery Shack, but instead of using a plan, he simply explodes a wall with dynamite.
Among the Looney Tunes directors, Bob Clampett loved this sort of thing, often justifying it with All Just a Dream. He directed "The Great Piggy Bank Robbery" and "The Big Snooze."