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!