Bart The General, specificaly episode three. For example, one of the subplots involves House — Yes, that House — in a well, calling out Milhouse (who was never in this fan series before) when a guy — He's possibly keeping House in the well in the first place — jumps down to have a conversation with him that's nearly incomprecencible, then lets him out. House then walks down a path to a desert while sad music plays, then finds a water tower with the letters "DB" writen in what seems to be yellow beans with eyes. While inside, a small floating thing smokes a cigar, and flys away while talking in a high pitch tone. It doesn't help that next to nobody talks clearly. Oh, and some of the names are changed for no reason and Bart-er... Berton looks like a creepy goth.
The Firefly fanfic Forward has this happen a few times in the "Riverthink" segments, usually when she's having her worst schizophrenic episodes. There were two entire chapters of the story that were nothing but River's POV, and more than one reviewer came out the other side asking "....I have no idea what half of that was about."
The Jubal Early hallucination in the "Fourth Interlude" is especially screwy for the reader, as he is alive and actively hunting the crew at that point in the story.
Two words - My Immortal. The fic originally starts off as an Author AvatarRelationship Sue dating Draco Malfoy in a gothic Hogwarts. Right aroung the bathtub scene does the story contort into a ghastly creature: Voldemort wears high heels and used to be a goth who dated Harry's owl (who is now a goth boy.) Ebony herself sleeps and tortures her way through the plot until she is given a time-travelling iPod. She is tasked with making Voldemort fall in love with her so he could stop being evil. After seducing Voldemort and leading him to have sex with Hedwig in the middle of the great hall, they both travel to the future, where Ebony, Draco, past!Voldemort, and Vampire have a four-way in front of Lupin and Filch for no reason. past!Voldemort then reveals that he knew about the time travelling all along, and reveals himself to be present!Voldemort. Then Snape crashes a flying car into the hall.
Peter Chimaera's fics in general can often veer into this territory, particularly when the spelling gets so awful that whatever meaning his words may have had is utterly obscured. His "Book of Hsitorical FaFfiction" contains such gems as "Caser was dysnnrf om yjr back" in the Caesar segment, along with this behemoth in the segment on Thomas Edison:
"...where goald beocomes makreasred aotuah of iraon oara leradrd buat thatsethe beatn and idraea that asd donra alreadsyt sor5 I daddiecdd not to write about it."
The fake ending of Latias' Journey, lots and lots of symbolism and surrealistic imagery.
The short King of the Hill vid simply titled hank hill (AKA hank hill.avi) [caps are correct]. Just... what? It's not even a minute long but still manages to be screwy. WARNING: Hank's comment at the begining is a little disturbing.
Everything else by Chris "Chriddof" Lyons, including the non-Fan Fic ones.
This How to Train Your Dragon fanfic, called "Of Oak, Ash and Blessed Thistle" is a good example of this. It starts out as what seems like an angsty Hiccup/Astrid romance involving an arranged marriage for Hiccup, but then Hiccup gets injured and has this freaky prophetic vision, and it all goes downhill from there. EVERY chapter contains some kind of subtle foreshadowing, most of which are so tied up with actual history and Old Norse that you need a guide at the start of every chapter to even begin to understand it...and you also have to use said guide to interpret what the characters are SAYING. Then halfway through, it seemed like the author suddenly couldn't decide what the main conflict of the story should be. So we have four or five different plot lines running around involving Hiccup's mom being some kind of goddess and wanting him to die because she sold his soul to Freya, Toothless being able to talk to Hiccup and Astrid, the village elder and Astrid's mom trying to trick Hiccup into getting Astrid pregnant, Astrid being royalty and not knowing it, a love triangle between Hiccup, Astrid and...Ruffnut? The list goes on until around Chapter 60, you finally say, "Hell is something gonna happen that MAKES SENSE?"
Nobody Dies, a Neon Genesis Evangelion fiction, pulled off an absolutely epic mind screw with the beginning of "Season 5" (Chapter 102): Everything since Chapter 70 was All Just a Dream courtesy of a planet-wide attack by Arael. Meaning that everything that happened since Zeruel was defeated... didn't happen. Except that some of it did: Uriel's still a Dominion, Zyuu's still human, and Armisael is still doing stuff just like he was in the Dream, so... what did or did not actually happen is kind of confusing at this point.
The rule appears to be as follows: everything in Australia or South America near Armisael actually happened. Arael either couldn't or chose not to deploy the field over those areas. Nothing else did, but if there was enough AT-field hax involved the effects on beings that existed already carry over. Anything that involved someone changing what type of being they are carried over. Anyone "born" in the dream was just an element of Arael's power, with the exception of the apparent younger copy of Ichi joining the original in the Mark-01. The stronger someones AT-Field is, the more they fully remember.
A certaintrilogyofJohnny the Homicidal Maniac fics falls into this category, deliberately cyclical enough to be a literal one of these. The disjointed and yet perfectly planned scenes, the horrifying realizations, the fatalism of watching it all play out... as Todd is supported by Nny in killing his parents, goes next door to find Nny afterwards, BECOMES NNY, forgets that he's Todd... and then it gets worse. It's Dark Fic of Johnny the Homicidal Maniac. That alone makes it a mind screw. Vasquez probably reads it for occasional laughs.
This fanfiction here: Fukakai-no-Unmei-, a Darker and Edgier version of Pokemon Mystery Dungeon Explorers Of Time. Where to even begin with this story? We start out with the human-turned pokemon main character and his partner who join a Guild that is actually a brainwashing, mind-raping cult that controls everyone whom they interact with, the cute little pokemon, Azuriwho is actually a Lab Rat used for experiments. It gets even WORSE half-way through when the main character dies. Please don't read the spoilers, people. Just enjoy the mind-screws.
A Shadow Of The Titans has the "Destiny" interlude, which breaks away from the main story to show an apparent Bad Future, where an adult Jade teams up with the Demon Sorcerers and Eight Immortals to stop an evil adult Jade from releasing something called "Omega", followed by an in-universe message of some kind that none of the readers understand.