Well this turned out to be harder than I expected, since Rachel's got virtually everything I would have mentioned over on her giant rec list! But I found a couple that escaped. :)
Don't Know How To Let You Go (NC-17) by merepersiflage. Post-Shadows Sam/Dean with angst, H/C, and resolution. Delicious, and so much more than just the sex.
Gather Me In Like A Rainstorm (NC-17) by dreamlittleyo. AU late-S3 Sam/Dean, atmospheric and somehow soothing.
keep the car running (PG-13) by aeroport_art. Sam/Dean, pre-series to S1 story in stream-of-consciousness that is somehow absolutely perfect and true. Very unusual storytelling.
Things My Brother Taught Me (NC-17) by deannaz. This is the first in a series of incredibly hot and schmoopy and perfect Sam/Dean dating from some underage years going forward. VERY satisfying series on all levels.
Atonement (PG) - Post-"Asylum" Gen H/C, with the resolution we'd all like to have seen.
Whispers From The Edge Of Sleep (PG) - S1 Gen that isn't exactly H/C or schmoop, but has a feeling I think will work for you. In a series of different dreams, Sam finds that the brotherly bond holds over time and form and danger.
Bedside Manners (PG) - Pre-series & S1 Gen. Even demon hunters get sick, and woe betide the people who live with them.
Great Reads for SPN/J2 fans in general:
I Wanna Hold You 'Til I Die (Sam/Dean, NC-17) by lazy_daze. Wonderful Curse!Fic, both funny and schmoopy.
All Out Of Sight(R) by whereupon. Gen Sam and Dean in a hunt gone bad. Gorgeous, painful, disjointed and perfect.
Parts Of Speech (PG-13) by mona1347. Gen, pre-series Dean without Sam, with a well-applied theme and gut-wrenching emotion. One of those stories I wish I'd written.
Always Some Door Open (PG-13) by dotfic. Gen S2 story with Dean and Henriksen swapping bodies, and the voices could not be more perfect here. Just fabulous.
Three Kisses In A Fucked-Up Friendship (R) by storydivagirl. Funny and hot, with some great lines.
Put That Thing Back Where It Came From (or so help me) (NC-17) by vorpalblades. How exactly does one create Jensen/Jared out of the Monster's Inc universe? Delightfully so, as it turns out. Wonderful humor and the storyline is genius, outweighing the need for a good beta-round. SO worth it. :)
True Love's Kiss (PG-13) by destina. Hilarious retelling of Sleeping Beauty as Jared/Jensen for j2_everafter, full of wonderful lines and, of course, a happy ending.
We Are Trains, Riding Hobo Style (NC-17) by silentpoetry1. Very unusual Jensen/Jared AU, just what the title says. A few tense-shifts, but marvelous overall, and it reads like dreaming.