Uncharted Desert Isle

It's short, Wincest, and fucked up. Sam's kind of peripheral and I didn't get much of a read on his character (I felt some distaste for him here, and I credit the POV with that one), but he's important. This is Dean's POV and he's a conflicted, violent mess, brilliantly done - yet I felt sorry for him, like in this version of the SPN world, Dean never had a chance. He's scary. No happies.
My Loose Thread by sasquatchbean

Title: Shattering The Cage by chokeonirony 
Pairing: Sam/Dean
Rating: NC-17
Summary: Sam and Dean find themselves and each other... via copious amounts of sex.
Warnings: Messy, unsafe and disorganised but generally consensual BDSM. Kinks including but not limited to d/s, dirty talk, voyeurism, orgasm denial, biting, marking, bondage, knife play. Also a fair bit of angst.

This is incredible, incendiary, much more than the summary would lead you to believe, and it's the author's first posting to the fandom. Unbelievable. It's not just about sex, but it's all about sex. This is about what's built and has been building, whole body, mind surrender, sensory surrender, trust and what it means to give all that up to another. Wonderful Dean POV.

I think someone said in the comments that we get a Sam without layers, down at his core. YES.  

Dean keeps holding his breath, watching him sideways as they drive through the village. But maybe for the first time Sam can understand how it feels to have a glass cage inside. How little it takes to shatter.

   

This is horror, guys, truly, so if you're a fan, I say step right up. It's also fantastical and full of imagery. The warning list itself is insane, but I don't think you'll end up rolling your eyes over it. It's one of those rare stories that actually earns the use of every one of those labels, even in passing. But it's still not about all that. It's imaginative and surreal.

Through the Valley of the Shadow of Death by losttheirbones 

January Sun by lemanya - features a young Sam and Dean and a lovely original character, December Jones.

from the story:

The house has been empty for as long as December can remember, but not ‘cause it itself is haunted. This town is a ghost town of the living, and no one wants to live here. This is where spectres exist in drawn out memories and glasses of bourbon. This is where people come to drink and smoke and gamble out the last of their days. They don’t come here to have any kind of future. In this town, wives leave their husbands and daughters are left on the front porch with the last birthday presents they’ll ever receive.
 

But the two boys and their father move a few bags and even fewer boxes through the door of the house across the road, and the house breathes again, light and bright. Beneath December, the varnish fades and the wood sits cold to rot.

God Says Nothing Back by mimblexwimble 
This is my favorite kind of story: hard hitting, dark, hopeless, word choice like strokes of paint on a canvas. Follows My Bloody Valentine.