Supernatural Fanfiction, Livejournal - Mostly Gen or Het (bleh) fanfiction, but some Wincest can be found here as well.
Wincest, Livejournal - All Wincest, all the time. Oh yeah! Lots of awesome fanfiction.
Sam/Dean Slash Archive - I don't think its updated much anymore but still lots of good fics to be found, great search features if your looking for something specific.
Fanfiction.net Supernatural Communities - Lots and Lots of different communities to choose from. Something for everyone. I really like the Dean Angst Archive myself, lol. Mostly Gen stuff, but you can find some Wincest here and there as well.