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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.
- 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.
- Buffy the Vampire Slayer: In the episode "The Pack", an exasperate Buffy tells her friends "I cannot believe that you, of all people, are trying to Scully me.".
- An X-Files type show exists in the world of GURPS Technomancer, in which Cat Morrigan and Dara Skuld investigate links between the government's stealth dragons and The Fair Folk.
- The second "Gangsters of the Underdark" spoof article in Dragon introduced two members of Sir Eliot of Kness's Forthright Band of Investigators named Vanyard the Fox and Danna the Skull, as well as vague mention of a pipeweed-smoking man.
- A Pyramid article for TOON called "The X-Fools" introduced TBI Agents Fax Muledeer and Dana Screwy, the Lone Punmen, and the Bubblegum-Chewing Man. The spoof is out there...
- 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.