Every Day in Every Way by velocitygrass
The first SGA Big Bang story I ever read. Rodney proposes he and John become "friends with benefits" -- until it becomes more. I love velocitygrass for her first time stories… and for her faithfulness in running mcsheplets every two weeks since forever.
In the Place of Jackals by auburn
Okay, it's only 18,500 words. An amazing story from Reverse Bang with art by danceswithgary. After a failed mutiny, the members of the Atlantis expedition are held hostage by the SGC while Rodney works for them. It's haunting and eerie... and Rodney. Just. Go. Read.
The Slow Slide of Indifference by ladyholder
Atlantis realizes that they are being abandoned by Earth and how they become self-sufficient. Until Earth changes its mind and want to force the Lanteans to return. They really become independent in the end. Great action and storytelling.