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.
Historical-Domain Character: Roy Cohn is the episode's major antagonist, and J. Edgar Hoover (in his second appearance on the series) gives a monologue outlining the Communist threat to Dales.
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.
Those Wacky Nazis: In a Call Back to "Paper Clip," Skur's first victim is an ex-Nazi scientist who's been performing genetic experiments for the US government.
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.