A few of my favourites:

Bonding Rituals: http://www.fanfiction.net/s/2558618/1/
Pick and Roll: http://remix.illuminatedtext.com/dbfiction.php?fiction_id=483
Six and Two: http://www.fanfiction.net/s/2841724/1/Six_and_Two
Two Tribes: http://www.fanfiction.net/s/2848638/1/Two_Tribes_Gone_To_War
Murder of Crows: http://community.livejournal.com/remix_redux/44753.html
Pretty Girl: http://community.livejournal.com/bsg_hiatusthon/6255.html (yeah, I know, but it just that good!)
Scenes from NC: http://runawaynun.livejournal.com/46322.html
Killing With Kindness: http://lochness.home.texas.net/fic1/KillingBSG.txt
Promises: http://www.fanfiction.net/s/3149195/1/Promises