I have literally just finished reading Sam I am (http://amberdreams.livejournal.com/395195.html)by amberdreams, just written for this year's Sammybigbang. Here, Castiel doesn’t immediately think of the idea of transferring Sam’s madness onto himself. As a result, Sam's brain is still fried. He escapes from the Westville asylum wing by himself, steals a car and drives until he runs out of road in Idaho. I really enjoyed the story!

I also recommend The puzzle that is me (http://archiveofourown.org/works/221671)by felisblanco. In this Jensen has Asperger's and in the author's own words 'it's as AU as you can get, while still having Jared and Jensen as actors on Supernatural.' There's also a sequel.

I hope these hit the spot! :)

Edited to say that Gunpoint (http://archiveofourown.org/works/861978/chapters/1652215), also by felisblanco would probably also fit the bill, but it does deal with some pretty heavy emotional trauma, so check the warnings.