I have a series of six fics where Dean has Asperger's.

Link goes to my master list, scroll down for the fics.

http://jennytork.livejournal.com/685519.html

There's minchout's Trip-Hop Verse (http://archiveofourown.org/works/995209/chapters/1968483): "This is the story of two people who find each other and try to make it work. Featuring Bipolar!Jensen and Artist!Jared."

In From the Cold (http://archiveofourown.org/works/449210) by ladyjanelly is a gorgeous story in which Jensen suffers from amnesia: "One thing about working in a free clinic, Jared thinks, is that work is never boring. You never know what'll come in from the cold on a night like this."

Jensen suffers from amnesia in Beholder (http://sandymg.livejournal.com/37314.html) by sandymg, too, which is another story I really loved: "Jared was passionate about the work he did with the animal shelter. Between that and living with Sandy, life was satisfactory. Until the cold night that the filthy, homeless man hidden in an oversized hoodie was dumped at the shelter and Jared couldn't just turn him out. Even if the man roared and called himself 'Beast.' Because under the hood, Jared was sure he caught a glimpse of a prince in those green eyes."

Oh and kalliel has a wonderful story about Dean with amnesia called Here There Be Tygers (http://kalliel.livejournal.com/206457.html): "The problem with Dean's memory is, it means he asks that question about eight trillion times more ("Sammy, are you okay? well, are you?") and as far as Sam's concerned, the answer matters even less. The problem with Dean's life is, it's supposed to end this year. And the problem with Dean's brother, well. Sam's still working on that one." (this one's gen)

And of course, if you haven't read In a Mirror Distorted and Indistinct (http://archiveofourown.org/works/222249) by felisblanco, go do that IMMEDIATELY: "They keep calling him beautiful. Pretty. “Come on. Look this way. Give us a smile, Jensen.” He smiles and blinks against the flashes, fighting the urge to lower his eyes, to hide the blush burning under layers of makeup. Sweat runs down his back, his hands tremble. He’s not pretty, not beautiful. He’s small and weak and pathetic and one day they’re all gonna figure it out. One day…."

Some more lists based on your tags: amnesiac!Dean (https://delicious.com/elwarre/amnesiac!dean), homeless!Dean (https://delicious.com/elwarre/homeless!dean), homeless!Jensen (https://delicious.com/elwarre/homeless!Jensen), incarcerated!Dean (https://delicious.com/elwarre/arrested!dean), incarcerated!Jensen (https://delicious.com/elwarre/arrested!jensen), mute!Jensen (https://delicious.com/elwarre/mute!jensen).

Does light-hearted bodyswap count? Sam/Dean; Keep Our Minds on the Sum of Each Other
http://lazy-daze.livejournal.com/452858.html

Have you tried Underneath the Weight of It All (http://users.livejournal.com/_mournthewicked/220635.html)by mournthewicked?

I was only looking for fics where Dean or Jensen was the one suffering from DID/MPD.

For DID/MPD:
there's Five (http://archiveofourown.org/works/3591723) by mira: "Even if Jensen's personalities have different ways to dominate him, they all love Jared just the same."

The United States of Jensen (http://archiveofourown.org/works/514829) by Takobella: "Jared needs a new place to live, and fast. Salvation comes in the form of a cute redhead named Danneel in his English class. Living in a huge spacious house with four other roommates seems like an ideal solution, but trouble has always found itself around Jared Padalecki, and this time is no different. He's had his whole live planned since he started University, but it looks like all it's going take is one man to knock it all down.

Jensen Ackles has been trying to fit in with everybody else for as long as he could remember. Broken from actions so horrible that he's blocked them from his mind, he lives in a world where the broken pieces of his self fight for control. He's managed to keep everybody he loves at a distance for all his life, but all that's about to change."

An interesting one is honeylocust's Run and Hide (http://archiveofourown.org/works/183079): "Soldiers have to be tough, son." This is Dean.

Mad-Server's "There is No You (There is Only Me) (http://mad-server.livejournal.com/39228.html)" is another Dean fic. "Dean does some thinking and some not feeling well. Sam, Cas and Bobby love him up. Concussion, angst, gratuitous head cold."

I'm glad that you asked for this, I just read "five" and was going to go look for more DID fic myself!

I see "Five" and "United States of Jensen" got mentioned already. Here's a third one: No Matter What (http://notyourpanel.livejournal.com/16827.html) - Jensen has Dissociative Personality Disorder (multiple personalities) and Jared is his boyfriend. Jensen's other personalities come out on occasion but it's all right, because Jared loves every part of Jensen.

Jensen with Aspergers - the puzzle that is me


http://archiveofourown.org/works/221671

I honestly can't recommend honeylocustree's work highly enough so... :) "At Bay" is a really excellent one where Dean's got schizophrenia and in "Run and Hide" he's got DID (both non-hunting AUs, sorry if that isn't what you were looking for).

At Bay - http://honeylocusttree.livejournal.com/880.html (http://honeylocusttree.livejournal.com/880.html)
Run and Hide - http://honeylocusttree.livejournal.com/28140.html (http://honeylocusttree.livejournal.com/28140.html) (Warnings for abuse)