Mind Screw/Fan Works

Chaos Is Very Good. And it's an understatement.
This Arthur fanfiction definitely counts.
- Especially in chapter 12 with not only an appearance from Simon Cowl and lopping Francine's hand off without her noticing immediately, some kids and him snort drugs while in detention. Seriously.
- And somehow they're all anime fans.
This, this, and this.
This has got to be one of the strangest Percy Jackson and The Olympians fanfictions ever.
This one's even odder.
Deep Water is an example of an intentional and well-done Mind Screw in Fanfic, by virtue of an extraordinarily complex villain with telepathic powers.
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 Avatar Relationship Sue dating Draco Malfoy in a gothic Hogwarts. Right around 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.
Paradigm of Uncertainty is a classic example, starting out relatively straightforward (as much as a fic featuring a post-graduation Harry Potter as a James Bond style superspy can be, anyway) but by the time we get to the second and especially third instalments of the door-stopping trilogy it's well and truly in Mind Screw territory.
"No! I must kill the demons" he shouted. The radio said "No, John. You are the demons." And then John was a zombie.
- 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.
Thirty Hs is a mind screw soaked in Squick and audaciousness. It's also completely epic.
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.
- While we're at it, pretty much everything else by Chris "Chriddof" Lyons, including the non-Fan Fic ones.
In a similar manner to hank hill.avi and Chriddof, Hank Hill teaches Bobbeh a Lesson.
Everything on this person's page. (WARNING; several of those stories are NSFW and may require Brain Bleach.)
This Family Guy....um....parody-thing.
Heta Oni, an Axis Powers Hetalia horror game based on Ao Oni. It includes Time Travel, memories that don't belong to them, Italy showing signs of being The Chessmaster, a Tony-look-alike Eldritch Abomination and an Ameriblob that keeps appearing!
Uninvited Guests chapters 37 and 38. This Bleachfic been bad enough from chapter one given the premise, supposedly hit its peak when Aizen got run over by an airborne BawaBawa, but as soon as Aizen figured out how to become The Hero, It Got Worse gave up and died. Especially his fight with Yamamoto in Chapter 38.
- And then Yachiru made Toshiro The Hero by pressing the "Shiro-chan" button on the thing that stole Ichigo's Plot Armor for Aizen. The guy who made it didn't put that there.
If this doesn't count, it ought to.
The author of Skin is absolutely in love with this trope. Reality itself is perfectly fine, but when Jonouchi starts having prophetic dreams...
- Because hey, bad enough knowing there's an Eldritch Abomination in that Artifact of Doom, but being able to see it?
The Anagram of Suzumiya Kurumi pulls this off in a good way. Without spoiling anything, let's just say it involves Time Travel, conspiracy theories, Anachronic Order, and even more crazy supernatural backstories for much of the cast than what was in canon.
He didnt want nothing to happen to Henry Freeman because Henry Freeman was John Freeman saw Combines start to run like monsters to humens and Henry Freeman and saw Henry Freeman and humens run like brave to Combines.
Th How to Train Your Dragon fanfic 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. Pretty much 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...not to mention that 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?"
The bizarre Pikmin video... parody... thing called 8min. You are not ready.
This Pokémon fic, it is totally random, and freakin HILA RIOUS!

Misty: NOOO! FAT NUMBERS AND FIVE PUDDINGS!

This Higurashi/Umineko fanfic. It takes an essay to even explain the concept of the story, let alone HOW it screws with you.
The Axis Powers Hetalia fanfic, Seven Little Killers. So, SO much.
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.