I am way behind on my recs, so i'll toss a few out and then try to edit this post to add a few more more.
I Gave Away What Wasn't Mine - by acidquill
Summary: John POV, insights into how John and Dean coped with Sam's leaving for college. great dialogue and turn of phrase.
Crossroads by eighth_horizon (one of my favorite writers)
Post-Scarecrow.Warnings: Dark, sad, mean piece of mental flotsam. Not a deathfic. More like character...destruction.
Losing Sam would kill Dean; but losing Dean would make Sam kill.
Summary: Sam tries hard not to think about how easy murder is, now. And then he reloads.
Where You Land by sevenfists
PG. Sam and Dean in California, after Jess.
A Crisis of Faith by geminigrl11
Post-Faith, Summary: The brothers face one of their darkest moments.
Go back, Jack (and do it again) by sxeraven
Post-Faith, Sam POV. "And I'd do it again, Dean"
The Sound of Silence by dodger_winslow
Post-Devil’s Trap. Summary: The silence is what you hear, and that’s what you’ll remember later.
So Tired I Can't Sleep by whereupon
Summary: From Palo Alto to a cabin so far out, nobody should be able to find it. Dean, Sam, and the road, all through S1. R.
In Want and Sympathy by iamstealthyone
First Person POV, Somewhat Smoopy Flu Story, Post-Bloody Mary
Summary: Sam, still grieving over Jess' death, gets unexpected insight into Dean's fears.
Never Not Once by estrella30
Summary: Pre-series, Sam at Stanford.
Don't Look Back by eloise_bright
Dean & John Winchester. Gen. Season 1 through Devil's Trap
(Personal Note: I adore the twist at the end)
Pinion by greensilver
Dean-centric; AU that splits off of Devil's Trap. Warning: includes heavy angst and (guest) character death
http://greensilver.livejournal.com/317397.html
A little left of center (and you'd have a whole other story) by lyra_wing
Post-Nightmware. Summary: Sam has a vision of a kid falling off a bridge. And wonders if he'll be next.