Let's see....
Every Day in Every Way by
http://sgabigbang.talkoncorners.net/?view=fic&id=8
The first SGA Big Bang story I ever read. Rodney proposes he and John become "friends with benefits" -- until it becomes more. I love

In the Place of Jackals by
http://sgareversebang.dreamwidth.org/21161.html
Okay, it's only 18,500 words. An amazing story from Reverse Bang with art by
The Slow Slide of Indifference by
http://www.wraithbait.com/viewstory.php?sid=10690
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.
Enjoy!