Recently declassified papers, dating from Area 51's heyday in the 1960s and 1970s are shedding light upon what exactly was so dang secret about the infamous military installation. We already knew that the U-2 spy plane was developed there, but let's just say that not every aircraft in the Area 51 hangars belonged to the U.S., technically speaking. Some of them were from much farther away than the authorities were willing to admit at the time.
Okay, okay, they were stolen Soviet MiGs. The U.S. government housed a number of "covertly aquired" MiGs in the hangar at Area 51 while conducting research into the enemy aircraft's weaknesses. One particular effort at exploiting am MiG-21 was dubbed operation HAVE DOUGHNUT (PDF).
The captured MiGs, as well as the secret U-2 spy plane, were so important to national security that the CIA actually ordered astronauts aboard the Skylab space station not to snap pictures of Area 51. NASA had the pictures taken anyway, against CIA wishes, and filed them away in Skylab's photo file, where somehow nobody bothered to find them and plaster them across newspapers world-wide.
Further documents were released concerning a number of aircraft known to have been tested at area 51. Among these were the F-117, the Bird of Prey (PDF) and TACIT BLUE( PDF). All in all, 60 new documents were released, with the most recent dating back only as far as 2009 (which confirmed the existence and mission of the USAF Sentinel drone deployed over Afghanistan, an aircraft which eventually became known as the "Beast of Kandahar"). You can find all 60 documents (and maybe even a passing reference to those aliens after all?) here.
National Security Archive, via Space.com