Documents recently declassified by the United States National Security Archive reveal that the secret Nevada test site was indeed playing host to alien craft... Unfortunately for conspiracy theorists, however, they weren't from another planet, but the Soviet Union.
Yep, that's what all the secrecy was about. Cold War politics. Disappointing, we know. But the documents do reveal some facts about the test site that are still pretty interesting. Rather than an extraterrestrial test site, the site designated Area 51 was in fact used from 1955 as a testing site for USAF aircraft, beginning with the Lockheed U-2 reconnaissance plane.
One of Area 51's later functions was the development of stealth plane technology, and ultimately the testing of one of the coolest-looking planes ever, the F-117 Nighthawk. It's actually understandable that UFO enthusiasts still bang on about the site. If anyone saw the thing being tested in 1981, they'd have had a hard time believing it wasn't from Mars or something.
The other type of top-secret activity going down at the test site was the US government's testing of both the capabilities and vulnerabilities of 'covertly-acquired' (probably fell off the back of a lorry) Soviet aircraft. One MiG-21, wonderfully-codenamed 'HAVE DOUGHNUT,' and two MiG-17s, 'HAVE DRILL' and 'HAVE FERRY,' were analysed at the base.
Of course, as UFO nuts will no doubt point out, 'Doughnut Drill Ferry' is an anagram for 'Dhudul Flying Terror,' and if that doesn't sound like an attack craft lifted straight out of Star Trek, I don't know what does. [NSA via Space]