IMHO it's simply a top secret air force research facility. No aliens or such stuff but instead other cutting-edge secret tech. Stealth crafts, UAAV and similar stuff, with the possibility of some tech "our very own" PHALANX had researched before closing.
That or it really is just an air force base. The area 51 myth could have been formed because of its "far-from-everything" location. Because of this it would also be a convenient distraction for the real secret labs.
Ps. All the big countries are bound to have some secret labs somewhere. Making better equipment in secret is better than in public (spies and such).
Edit: Oh yeah, I'm answering that "thinking" part, as I've never been in USA.