Running Laps Around The Sun by pixel_0 (Wincest, Adult, Season 2 timeframe, unrelated to finale). This is a heartbreaker of a story that'll get right on down inside you and ache as unfolds so perfectly. Sam decides to go back to Stanford after all, and it's the way Dean helps him do it that'll have you reaching for the Kleenex. Told from Sam's POV, and how the reader knows everything Dean's feeling, even while Sam misses it, is so skillfully shown. Angsty, compelling, and the ending is full of beautiful resolution that makes it all worthwhile. You'll end on a happy note.
For I Have Sinned by miss_begonia (Jensen/Jared, NC-17, Drama). This story struck such a chord with me, with its incredible use of an over-arching theme and how that returns again and again to control the action. In this universe, Jensen has grown up in a religious household where the idea of wanting other men is an abomination. He's spent years pushing that away, pushing any real thoughts of love away, until there's hardly anything left that's still him. When he meets Jared, he gets further and further lost as every part of him wants what he shouldn't, as his happiness lies just there beyond his reach. The incredible ache and loneliness of the Jensen in this story will really take hold of you, and you'll want Jared to find him more than anything. For me, this goes beyond fanfic-- this is writing as an art.