Wonderful Inventions (http://tcs1121.livejournal.com/20327.html#cutid1) by tcs1121. Unfortunately, I don't remember if it's bottom!Jensen. :( Maybe you can skip the scene if it's not because it's a great fic, I highly recommend it.

Summary: The quirky, absent-minded, yet brilliant Dr. Jensen Ackles created big, successful, life-saving inventions. However, while working on his newest project, he was struck down by a devastating illness, leaving Dr. Ackles still quirky, absent-minded and brilliant, but...happier.

Misha, Jensen's long-time professional and personal assistant, now helps Jensen manage his delusions, seizures, and hallucinations, which Jensen takes in stride. But when Dr. Ackles picked up Tristan one morning by the Boardwalk, professing an unexplained yet all-encompassing love for the street walker, Jensen became happiest of all. He loves his life, his life, his life.

Until the court tries to take it all away.

thanks!

My favourite Aspergers!Jensen is The Puzzle (That Is Me) (http://felisblanco.livejournal.com/1039042.html) Summary: As they start filming and working together, Jared realizes Danneel’s prediction was right. He and Jensen do hit it off. Sure Jensen is quirky and sometimes (okay, a lot of times) uncomfortably direct to the point of being rude. But once Jared figures out Jensen isn’t actually mean as much as he’s just a little clueless (and mostly unconcerned) about the rules of social interactions, it stops bothering him.

Love Lies Burning (http://archiveofourown.org/works/448327) is a wonderful fic where Jensen has elective mutism and neurological disorder/borderline Aspergers.
Summary: Jared Padalecki heads up one of the largest companies in the mix and bake market. He is ruthless, devious and successful. His personal assistant, Alona, will tell you that he’s an asshole. His best friend Misha will agree. When a Padalecki factory burns down, killing the homeless squatters inside, Jared finds out he has a stalker and his life starts to spiral out of control.
Jen knows he’s wrong, he’s never been right. He stays quiet and watches from the shadows, until the night a fire illuminates his presence. He suddenly finds himself having to face a reality he’s been avoiding for years.
In short, it’s a tale of obsession, deceit and danger, with a pissed off personal assistant …. and cupcakes.

thanks!

Can't leave out sandymg's ONE SMALL STEP with Asperger's!Jared - one of my favorites.
http://archiveofourown.org/works/255856

Thank you for the rec for Wonderful Inventions, herminekurotowa! (To the OP, it's J2 but no sex, so don't worry about who bottoms :-) )

Two of my favorite mentally challenged, and coincidentally , Homeless!Jensen stories are:

sandymg's Beholder (http://sandymg.livejournal.com/37314.html)

Summary: 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.

and ladyjanelly's In From the Cold (http://archiveofourown.org/works/449210)

Summary: 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.

And, to paraphrase herminekurotowa, I don't remember who bottoms, but they are both wonderful stories.

PS. I second sandymg's One Small Step (http://sandymg.livejournal.com/60559.html). It's one of my favorites.

thanks!

The Colors of My Life (http://tcs1121.livejournal.com/25122.html) - Best blind!Jensen fic I've read ever and it's J2.