The whole alien thing at Area 51 is just ludicrous. It's just a place where the USAF tests its new planes. But, given the whole amount of secrecy surrounding the place, nobody can be too sure...
Speaking of Stargate SG-1, Helios is right. The Stargate is in Colorado. But Area 51 could be the place where they do research on the Goa'uld, the Tok'ra, and the Asgard, among the species represented in that show.
P.S.- Other stuff the government might be working on in Area 51*:
- Zerg
- Xenomorphs (secret conspiracy w/ Weyland-Yutani, perhaps?)
- Predator (w/ an emphasis towards the weapons and cloaking device)
- Wookiees (and just about every race in Star Wars that isn't either near-human or a human subspecies)
*This postscript is a complete work of fiction, OK? Don't be getting any weird ideas!

And that ends my crazy little rant. I know I'm practically condradicting myself in the first part, but that's the way it came out.