Area 51

Area 51 was first mentioned in Framed and later appears in Prisoner Number 775 is Missing. Lieutenant Steel works at (or at least knows about) Area 51.

Area 51 appears at the beginning of the episode Prisoner Number 775 is Missing, where Old George arrives at this place, after knocking out the guards, George entered one of the warehouses. A bright yellow light glows inside the warehouse that explodes causing Area 51 to completely disappear (as Cooper explained no crystallized glass so it wasn't teleported and no scorch marks so it wasn't blown up). It is then discovered that there is actually an alien prison located underneath the base itself that has been in commission by the United States Government for around 50 years, a facility designed to hold "alien combatants" on charges of being a possible threat to humanity.

Trivia

 * A parody of Area 51 is Area 42, a military base from the game Destroy All Humans!
 * Another parody of Area 51 is Area 99, a G.U.N. research and development facility from the Sonic X Anime.
 * Area 51's name also resembles to Area '51.1' from the animated cartoon show Johnny Test.