Apologies for the double post, but I can't seem to edit my post above. Found the other fic I was looking for where Sam is raped/abused. It's:

The Missing by mentholpixie
Summary: 'Sam wonders if Chet kept the others this long and if they wished for death, too. He thinks that if he could talk to Dean maybe he'd tell him that he's already too late.'
http://mentholpixie.livejournal.com/8407.html#cutid1