1: After Midnight, by jillmariej
Jared and Jensen have known each other since they were kids, but Jensen's home situation is such that he escapes despite the fact that he is in love with Jared. When he finally decides to go home and look for his lost love, he is a very different man from the troubled youth who ran away. This story borrows a little from Grosse Pointe Blank, but it's a very different story, and one that sucked me in from the start.
2: This November Life, by yourperiphery
Dean has just done a deal with the Crossroads Demon to bring the brother he adores back to life. As it happens, Sam is not impressed. The LJ is gone but the story is still up if you click the link.
3: Domestic Bliss and Other Oxymorons, by yourperiphery
Another story by yourperiphery , this time J2 and rather funny. Set back during Seasons 3 and 4, it documents the boys' relationship at that time and then goes AU in a most satisfying way. The conversations between Jensen and his mother are really funny.
4: The Right Angle, by tebtosca
This is poetry. Jensen is closeted, and a one night stand helps him come to terms with who he is. It's beautifully written and it doesn't pull its punches.
5: The Iron Tongue of Midnight, by zara_zee
Sam and Dean AU, and definitely NC17. This is a really intricately woven story set during Sam's Stanford days. Sam is not a Winchester, and he's struggled his way out of a life of prostitution to start making something of himself. He's forced to turn one final trick to pay off a debt, and that's when Dean picks him up to persuade him to take Dean's place in a faerie ritual.
6: Like Tears in Rain, by ysbail
This is a take on Blade Runner, with Jared hunting replicants one last time before he retires and Jensen questioning his own identity.
7: Cardinal Hunter, by zubeneschamali
Perfect Sam and Dean au crossover with Pacific Rim. When the Kaiju begin to invade, and Stanford is flattened by an invading monster, Sam joins the team to become a Jaeger pilot along with Jess. Dean goes along as an engineer, and as the Kaiju become stronger and stronger, the Winchesters have to work together. Can they save the world, or will it go down in flames?
8: And the Complications You Could Do Without, by ygrawn
This is Sam's point of view. It isn't complicated at all. He just wants Dean to kiss him. Dean will do everything else, but Sam wants to kiss him, and he doesn't understand why Dean just won't.
9: I Wonder Why the Wonder Falls on Me, by zannes
Brilliant crossover-fic featuring Sam and Dean meeting up with the Tyler family as they invade the world of Wonderfalls. Wonderfalls was a short lived series that was not given a chance. It aired about 4 episodes and was yanked at the same time as Firefly. it was one of the funniest, weirdest, cleverly written shows, and I suspect that it would've lasted much longer if it had been launched today. Sam and Dean think that their family is odd, but they haven't met the Tylers yet...
10: Riders on the Storm, by zempasuchil
This is a wonderful character study of Sam Winchester and his relationship with his brother. It's angsty, hot, sad, happy... everything you'd want in a long, meaty story with a whole lot of canon thrown in.