Before My Time: In "Travelers", Mulder goes to interview a retired FBI agent who investigated X-Files in The Fifties. The agent asks Mulder whether he's heard of the House Un-American Activities Committee, but immediately assumes that he hasn't. Even if he knew nothing about Mulder personally, the topic is covered in high school history classes.
Red Scare: The episode's backdrop: Edward Skur is arrested for alleged Communist ties, and Roy Cohn and J. Edgar Hoover even appear as characters.
Title Drop: Unsolved cases were filed under "U", until space in the filing cabinets ran out, so they were then put under "X" which had extra room. Thus, the unsolved cases are "X" files.