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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.