Geeze, I can't believe I hadn't recc'd this yet; it's one of my all time favorites. In fact, I thought I had, but no...
Story of a Girl by seperis is a Stargate Atlantis (John/Rodney) genderswitch story. (And I just have to say that I absolutely adore Joan Sheppard.) In this universe, Joan Sheppard is the Air Force Major that goes to Atlantis and becomes the Military Commander. As a woman, she has to work even harder than John to get the respect of the Marines, but she does have Teyla's help. As for Rodney, well, it seems no incarnation of John Sheppard is immune to Rodney's own particular brand of charm.
Hindsight by rageprufrock (that was the name on the email, anyway) is an SGA AU Rodney/John slash story... and the story that dragged me into SGA fandom. I've been avoiding it for years, mostly because the character of Dr. McKay so annoyed me in both the SG-1 episodes he was in and the first few episodes of Atlantis. However, in fan fiction, I discovered that he's much easier to take. Also, I'm completely smitten with John (and Ronan and Teyla are very cool). Anyway, in Hindsight, John is an FBI agent rather than an Air Force pilot. The reasons for this are slowly revealed in the story, so I won't go into it now. But this story completely rocks.