My favorites are leonidaslion's One Going on Eternity and Counting (http://community.livejournal.com/leonidasden/26113.html?style=mine) and alazysod's Sharing Different Heartbeats (http://alazysod.livejournal.com/222359.html?style=mine). They both have happy endings.

This is more a case of very bad timing and angst, but I hope you like it...
If It Ends Now, let the Words Remain Unsaid.
http://verbalavalanche.livejournal.com/5938.html

When I need a very fast (but tasty!) hit of Dean's pining and man-pain, I re-read astolat's Loud and Clear (http://www.intimations.org/fanfic/supernatural/Loud%20and%20Clear.html). Happy ending!

Okay here's one with serious man-pain, a case of sam wantind dean and dean giving him what he wants, super-angsty, dub-con at the very least: http://www.fanfiction.net/s/2777969/1/Unholy

Very good, very angsty....but no happy ending here :(

Self-pimp! I wrote unrequited wincest (warning: unhappy ending): Morning in the Evening (http://ivy03.livejournal.com/237590.html) and sequel Crazy Faith (http://ivy03.livejournal.com/251415.html)

this one breaks my heart. I've read it before and oh god it rips me into tiny pieces SO GOOD.

I went through the five stages of grief after this fic! I never got around to the acceptance part, I just block it out of my mind. When she says unhappy ending, she means it! It's gorgeous and powerful and heartbreaking, and I recommend getting some comfort food or schmoopy fic lined up to help you recover.