One that you absolutely have to check out is Fade To Black by Phx69: http://phx69.livejournal.com/34841.html
Summary: Blurb:  Roosevelt Asylum was Chicken Soup for a Brother's Soul. Compared to this.

In this one Dean is possessed and er ... Yeah Sam suffers quite a bit, its really dark & it's a great fic :)

If you want really really dark Sam torturing Dean, I'd suggest tifaching's accoustic verse

Gorgeously written, but horrifying on poor Dean's part. Sam's taken over by his evil side and Dean suffers the consequences.

Three Days on the Rack: http://archiveofourown.org/works/221235?view_adult=true

His Pretty Lips, Another's Lies: http://ladycrystal-c.livejournal.com/9959.html

Here's something really rapey and explicit, where Sam is possessed and rapes Dean in a warehouse: "Wish I could forget" by starvingartist114:
http://www.samdean.archive.nu/viewstory.php?sid=2184

Another one, in which Sam rapes Dean repeatedly, then wipes his memories with his psychic mojo (really sad ending): "Non timebo mala" by spnlover89:
http://www.samdean.archive.nu/viewstory.php?sid=2626

Really dark and sad fic, in which the boys are caught in the Trickster's TV land and Sam has to rape Dean (fuck-or die scenario), and ends up liking it: "Just a role" by ash_carpenter:
http://ash-carpenter.livejournal.com/132618.html

One in which a shapeshifter that looks like Dean rapes Sam: "Shifting" by tazzyjan:
http://www.samdean.archive.nu/viewstory.php?sid=843

Enjoy! ;)

This kind of fits what you are looking for: dark, torture, it has a happy ending (sort of).

I Found My Brother and I Found All Three by the_brat_i_am

Dean made a mistake many years ago, a mistake he tried so hard to bury, one that drove Sam to abandon the people he loved most. Now, the demon knows their secret, and he uses it to warp Sam, leaving Dean to deal with the aftermaths. There was a time Dean Winchester would have done anything for the family he's running from. Anything...

http://the-brat-i-am.livejournal.com/7244.html