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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.
- In the Goosebumps book Return to Horrorland, Margo Strange is directly compared to Scully.
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.".
- The band Eve 6 took their name from the episode "Eve".
- The Catatonia song "Mulder and Scully".
- One of the many pop-culture references in the Barenaked Ladies song "One Week" is "Watching X-Files with no lights on"
- Bree Sharp's hit song "David Duchovny" about a fangirl with Celeb Crush on David Duchovny and Perverse Sexual Lust to "secret agent man" Mulder. She got those two all confused and she mixes the show with reality.
- At the start of the Beyond Treasure Hunt semifinal match between "The Galaxy's Greatest Alien" Kris Statlander and Jordynne Grace, one of the commentators said "I want to believe" and the other said, "OK, Mulder."
- At WWF In Your House 17: Ground Zero, September 9, 1997, "The Loose Cannon" Brian Pillman defeated Goldust in an Indecent Proposal match, meaning he got Goldust's valet (and then-Real Life wife) Marlena for 30 days.note During this time, Pillman showed videos on WWE Raw of himself and Marlena titled "Pillman's XXX Files."
- 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...
- In Stay Tooned!, the channel surfing portion at the beginning of the game has a promo for The XXX Files, with the tagline, "The naked truth is out there.".
- Phantom Doctrine: You can find a document in which a spook suggests that "our friends in Hollywood" make a TV show about an agent who investigate ghosts and aliens and conspiracies. Plots would include distorted versions of real conspiracies, so that if investigators uncover those, people will accuse them of getting their ideas from TV.
- 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.