In the special features on one of the Atlantis dvds one of the writers talks about how theres like 6 sci fi stories and everything just tries to do each of them in a new way. I think it was something like 1: Aliens, 2: Time Travel, 3: Nanotechnology, 4: Virus, 5: Alternate Dimension, 6: Robots.
They've even combined a few. I think really the only plot they haven't done on Stargate is Alien nanomachine robots from an alternate dimension going back in time to infect us with some crazy virus.