Yeah, like Astrogeek says, Area 51 is (or was) most probably a test ground for next generation U.S. Air Force aircraft.
I say "was", because they probably do not test their stuff there much any more - too many enthusiastic UFO believers lurking around and filming everything… :-)
I bet they tested the F-117 stealth fighter, B-2 stealth bomber and their prototypes there during the 1970's and the 1980's (they went public in the Persian Gulf War in 1991).
I also bet that what they are testing now has probably something to do with next-generation robotic UAV's (Unmanned Aerial Vehicles), like the next iteration of Predator and that sort of things. Maybe an unmanned fighter-interceptor concepts or something like that.
But no, not UFO's or aliens.