The Freak Camp Verse (http://archiveofourown.org/series/5884), if you haven't read it, by brosedshield and lavinialavender is horrible and dark and wonderful: "The same old Sam/Dean love story, with a darkfic twist. Sam grows up in a concentration camp for monsters, and Dean is raised as an only child and a hunter. Together, they make each other human." (Sam/Dean, tons of Sam hurt and abuse, I think? bottom!Sam, but again I'm not sure)

Non Timebo Mala (http://archiveofourown.org/works/273894/chapters/433454) by roxymissrose: "This is my very AU version of the Colt's making. It's completely a child of my wild imaginings, thus expect anachronisms, improbable situations, and flagrant display of personal fanon. This can be seen as an alternate universe, or an alternate timeline." (Sam/Dean, hurt!Sam, bottom!Sam)

Inviting the Dawn to Break (http://paper-storm88.livejournal.com/59918.html) by paper_storm88: "When Jensen first realized he was gay, he had some silly, fairy-tale notion of meeting an amazing guy and falling in love, but then he discovered how much fun sex is and that’s always been his endgame since. When he looks at Jared, he feels like he’s eighteen again; starry-eyed and hopeful and dreaming of creating a life with somebody. It should be frightening him down to his core, because all those things go completely against the way he’s lived his life for the past seven years. But then he remembers Jared’s smile, or the way he smells, or how big he is and how good Jensen imagines he’d feel pressed up against him, and then he doesn’t care about anything else anymore." (Jared/Jensen, abused!Jared (past), bottom!Jared)

I've saved a whole bunch in these categories, so here's some lists for you (they're generally pretty well-tagged with the pairing and who tops/bottoms, etc):

sick!Sam (https://delicious.com/elwarre/sick!sam) || sick!Jared (https://delicious.com/elwarre/sick!jared) || abused!Sam (https://delicious.com/elwarre/abused!sam) || abused!Jared (https://delicious.com/elwarre/abused!jared) || hurt!Sam (https://delicious.com/elwarre/hurt!sam) || hurt!Jared (https://delicious.com/elwarre/hurt!Jared)