In my early days of SGA fandom before I'd seen much of the show, I responded to AU recs more, so maybe it's my own predisposition influencing my memory. But to me, some of the stories that seemed widely read by people who didn't know the fandom well were Strangers on a Six Train, Junk Cheap, 101 Ways to Get Lucky In Love, and the Farm in Iowa series.

Oh, and Hindsight and Ladies' Night At the Boom Boom Room and the Atlantis Stitch-n-Bitch Club stories by Rageprufrock.