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- In Independence Day, a television customer service representative talking to a customer who's angry about service disruptions tries to calm them by saying that he likes The X-Files too.
- In Odd Thomas, Odd's girlfriend Stormy calls him Mulder when she thinks he's being overprotective. He only calls her Scully if he's willing to get smacked for it.
- In Girlfriend In A Coma, Richard and his friends wind up working on an unnamed television show that's obviously that world's version of The X-Files.
Live Action TV
- Castle did a whole episode to homage The X-Files. Castle whistles the theme song, Becket is called Scully, they become entangled in a government project, and the villain is called the cigarette-smoking man.
- Bones: When Bones and Booth investigate a weird case, the theme songs starts playing... Too-doo-dooo-DOOO-dooo... Turns out it's the victims mobile phone.
- Home Improvement: Jill and Tim played Mulder and Scully once.
- Buffy the Vampire Slayer: To scully somebody means to try to rationalize something when a paranormal explanation is more plausible.
- Supernatural had an episode where the Monster of the Week originally appeared to be aliens, for which they changed the title sequence to resemble that of The X-Files.
- Breaking Bad has an episode titled Cancer Man. Vince Gilligan, creator for the series, was a frequent writer on The X Files, which has a character called The Smoking Man. Cigarettes give cancer.
- Crusade had an entire episode, "Visitors From Down the Street", devoted to parodying The X-Files, via the introduction of a conspiracy theory-themed Planet of Hats.
- Agents Wolf and Cranium, the two government agents in El Goonish Shive who are highly skilled at hushing up aliens and magic, and completely inept at hushing up their relationship, are a pastiche of Mulder and Scully.