Amazing story written on Fanfiction that I think you'll like. I love re-reading it, has all that your looking for. Its Hell Can be Home Too-> http://www.fanfiction.net/s/5843811/1/bHell_b_Can_Be_Home_Too

Great story, i think you'd like it.

The Suite Verse by Leonidaslion immediately comes to mind
http://archiveofourown.org/series/6436

And a bunch of other fic by Leonidaslion. I can't name any as my memory sucks, but there are a couple more, I think.

Seconding Suiteverse, though by now everybody and their (gay incestuous) brother has probably read it....but if you haven't, it's a must if you like dark Sam goes evil for Dean stories.

You should also check out sammessiah if you haven't yet. It's a comm devoted to evil Sam, and many of the fics collected there have sweet little Sammy only turning evil because he's misguidedly trying to save Sam. (Though sometimes not...)

I wrote one based off of a wonderful dark!Sam vid. Sorrow Enough to Drown the World (http://gestaltrose.livejournal.com/44470.html)

The most beautiful story I can think of to match your search is
"If you burn away (I'll pray to the skies above)" by taelyn_hawker:
http://taelynhawker.livejournal.com/22614.html
Dean dies and Sam goes against his brother's dying wish, losing himself in the pain of his brother's death and becoming something Dean never wanted him to become. Now the end of the world has begun. Dean comes back to find his brother is someone, something, he doesn't know or recognize. Sam's determined to get Dean back and then take on Lilith. Dean just wants to save his little brother.

This is an awesome story: A Three Fold Path to Redemption by Rei C

http://rei-c.livejournal.com/952440.html

That's the link to the first story. This blew me away

Seconded! This one invaded my mind!!!

Now We Are Come to Our Kingdom (http://cormallen.livejournal.com/98718.html)
It's been months since Dean sold his soul, and Sam's run himself ragged trying to find a way out, Chinatown to "Amber Moon", South Dakota to Connecticut. So far he's got nothing to show for it but some cryptic words – "You've got the 'what' and the 'where' and the 'when', and you think you're missing the 'how'. You aren't, of course, only you haven't figured that out yet." There's a possessed girl following him around, Dean's trying his hardest to drive Sam insane with jealousy, and the visions that were supposed to stop when Azazel died still wake him night after night after night.

Bad Company (http://delanach.livejournal.com/23675.html#cutid1)
Dean’s deal comes due, and he goes to hell, but not for long. Heartbroken, Sam taps into the power inside himself to save his brother, and drags him out, but not before Hell can leave a taint on Dean’s soul. When Dean comes round at Bobby’s, it’s to a very different world to the one he left. The dark power inside Sam corrupted him, and now he rules not only hell, but a shattered world where his word can mean death. Dean reluctantly becomes a leader and has to find a way to save the world from the brother he still loves.

Stop Thinking (http://extraonions.livejournal.com/15829.html)
There are only so many lines Sam can cross before he won’t be able to stop walking. AU Evil!Sam Future!fic.

Tricking (http://rivkat.livejournal.com/197549.html?format=light)
Dean's permanent record has the facts, but not the truth. Sam has some trouble with the difference.

Shades of Mine (http://dreamlittleyo.livejournal.com/21772.html)
Sam's destiny doesn't quite go as planned, and when things get darker, Dean doesn't try to fight it.