I had a grandfather who was in the air force. He told me countless stories of seeing UFO's (he grew up in nevada and flew in the air force and air natl guard all over the southwest). He also had SOME top secret clearance and he also flew into area 51 every now and then. He told me he doesnt think there are aliens at A51 or anything of the sort. His reasoning for all of the strange sightings were top secret government projects.
Thats what I tend to believe. If the AF is testing some awesome new technology its not crazy to think that PHX would be in the flight paths from time to time.
BTW- My grandfather flew in an F-104 from vegas to phx in about 9 minutes (mach 2.5). Not bad eh?