That's a REALLY tough choice. Thankfully the other reccers already mentioned some of my favorites, so that made the task a little easier. I'm a Dean girl, so both these are Dean-centric:

Named (http://archiveofourown.org/series/50452) by RC_McLachlan - amazing, vivid storytelling, riveting plot with perfectly in-character Team Free Will and very cool original characters. There are scenes from this fic that I'll never forget.

The 1300 Days (http://archiveofourown.org/works/695225) by stele3 - again, incredible storytelling, great plot with some of the most interesting and original (and loveable, in one case) OCs I've ever seen. Plus lots of hurt!Dean but also competent!Dean and BAMF!Dean.