These two by leonisdaslion:
The Light of Munin (http://archiveofourown.org/works/180210/chapters/264948)

The Bright Lights of Disturbia (http://archiveofourown.org/series/7424)

And many of her other fics have similar dark themes.

And here is the
Evil!Sammy Universe (http://writingbyebonio.livejournal.com/7233.html) where we see the break down of Dean and sort of see Sam's. It's wip, but very long already.

I've read all of Leonisdaslion's fic, but thanks. For the Evil!Sammy universe, is Sammy the bad guy? I can't handle one of the boys being mean, I probably should have stuck that in the request!

In the Evil!Sammy verse Sam is kind of the bad guy. We see everything from Dean's pov, so we don't know what's going on all the time. And the verse is told out of order, so we find things out later.

But look here if you want to know more spoilers:
Sam has his reasons, but does bad things-how much outside of what he does to Dean-we don't know. Sam goes missing from Dean for a while, and it turns out he was kidnapped and was brainwashed and tortured by some bad guys (demons, others with powers etc). We don't see much of what happens to him. They make him so afraid of them (and brainwashed of course) that he goes along with their plan of taking over the world. He wants to protect Dean, but the only way he can think of to do that after being so damaged is to make Dean insignificant to anyone who would want to hurt him and basically make Dean his property (slave). So he does sexually abuse him and lock him up, and is basically conditioning and brainwashing Dean-though Dean is fighting it and trying to figure out what's going on exactly because Sam won't tell him. So it's a very dark fic. But I still have some hope.