I think this one had that, but it's been a while since I read it:

After Sam
by AmberDreams - Cicero has been quiet and safely boring since the changelings, but now something is stirring in the depths of the reservoir.
http://www.fanfiction.net/s/6408295/1/After_Sam

There's one where Dean keeps getting sick after the Apocalypse, although he NEVER got sick before. He keeps punishing himself for what happened to Sam and eventually ends up in the hospital with bleeding ulcers. I forgot what it's called, though.

Hey, thanks a lot! Gonna check it out as soon as possible!!