Vince Gilligan was a fan of the show before joining the writers. He even followed the filming of his first episode, "Soft Light", with his personal camera.
The character Leyla Harrison was introduced as a posthumous tribute to a well-known Fan Fiction writer of the same name.
A smaller example: fans on the official messageboard were listed on the manifest of a crashed aircraft in a later season.
In the season 5 finale "The End", the extras who filled the stadium in the teaser are all recruited from the X-Philes. That's right, X Files fans were filling up stadiums.
Cast the Expert: The episode "The Amazing Maleeni" features two stage magicians, both played by actual stage magicians.
Dawson Casting: Inverted with Agent Scully; she was born in 1964 while Gillian Anderson was born in 1968.
Fake American: Gillian Anderson was born in America to American citizens, but she moved to England when she was two and didn't move back until she was eleven, and by then her speech patterns had been set. She had to work to lose it when she went into acting, and if you pay attention to the early episodes of The X-Files it slips through at times. Now that she's moved back to England, she's got the accent back in full-force. Her American accent she acquired in her teenage years comes back whenever she's interviewed by an American reporter.
Fandom Life Cycle: Definitely one of the very few that went through the whole cycle and reached the mainstream recognition. Even people who never watched a single episode are likely to know who Mulder and Scully are.
The Organization: The sinister group that consists of many adjectival men and who the Smoking Man works for.
Cigarette Smoking Man, a.k.a. Morley Man (after his preferred brand), a.k.a. Cancer Man. "Cancer Man" eventually started being used in the show itself. "Marlborough Man" has also been used, after the source of the expied brand used in the show and the spokes-character introduced to sell it after it was switched from being a woman's brand.
Ratboy: Krycek. Also known as Skippy.
The Schwarzenalien, the Mighty Morphin Bounty Hunter. Shapeshifting alien played by Brian Thompson.
The Fowl One: Diana Fowley (also referred to by more colourful names).
Plam: The knife with the retractable blade that the show implied was THE ONLY weapon that could kill the aliens. Named from a moment when Mulder's mother was trying to tell him she'd hidden one in her lamp - but she'd had a stroke, so "lamp" came out "plam".
Franchise Killer: The second movie is suspected of being one, although after a ten-year gap could be considered more of a failed attempt at resurrection.
Peter Boyle plays a psychic who can only predict people's deaths in "Clyde Bruckman's Final Repose". He won an Emmy for "Outstanding Guest Actor" for that episode, and was his only win out of 8 nominations, including 5 from Everybody Loves Raymond.
Lying Creator: Word of God said Mulder and Scully wouldn't ever kiss. Watching the show comes to convey the contrary. Word of God also said that there would never be any romantic relationship going on between Mulder and Scully, before admitting after the show's run that having them together in the end was the original intention. Word of God is a big liar, basically.
The Pete Best: Not the same character exactly, but the principle applies: Charles Cioffi as SCI Blevins, Mulder and Scully's boss in the Pilot and Conduit, was intended as a regular character but Cioffi proved unable to continue in the role (though he did reappear in the Gethsemane/Redux arc in Seasons 4-5). He was replaced in Fallen Angel by the one-off character Section Chief McGrath, played by Frederick Coffin. Finally, Mitch Pileggi played Skinner in Tooms and the rest is history.
Reality Subtext: In "Hollywood A.D." a film producer decides to make a movie based on Mulder and Scully's adventures, casting Garry Shandling and Tea Leoni for the roles, respectively. Scully mentions to Mulder that Leoni may have a crush on him, which he considers ridiculous. Any guesses to whom David Duchovny is married in real life?
They reworked season one episode "Ice" (about a parasitic alien that caused its victims to turn psychopathic and eventually die) into the season two episode "Firewalker" (you can probably guess the main difference). Both were based, in turn, on the classic John W. Campbell short story "Who Goes There".
"One Breath" and "Audrey Pauley," aired seven seasons apart, are almost exactly the same episode, just with a different partnership in the spotlight. Both involve the female half of the team (Scully and Reyes, respectively) falling into a coma after a traumatic event, and eventually being declared braindead. While in a coma, they have their own sub-plot on a different plane of existence. Meanwhile, the male half of the team (Mulder and Dogget, respectively), run around trying to figure out the paranormal aspect of the episode, as well as try to find a way to bring the female half of the team out of the coma and threatening bodily harm to those who attempt to shut off life support. There are a few minor differences: "One Breath" was part of the show's Myth Arc while "Audrey Pauley" was season 9 filler, "Audrey Pauley" had a more clear-cut paranormal aspect to it, and the causes of the coma are quite different. However, the scripts are so similar that in some scenes, Doggett repeats Mulder word-for-word.
Of course, this also brings about a few Funny Aneurism Moments. While "One Breath" was meant to show the deepening bond of Mulder and Scully's friendship, "Audrey Pauley" was used explicitly to showcase Doggett and Reye's romantic relationship. Using almost the exact same script. It also make's Scully's unsympathetic nature towards Doggett rather ironic — she is the one making the arrangements to take Reyes off life support and donate her organs, and thinks Doggett is crazy for trying to save her. It's Justified in that she was in a coma for almost all of "One Breath" and didn't see Mulder do the exact same thing, but it's still makes her seem like that much more callous.
Under Age Casting: Gillian Anderson was cast as Dana Scully at twenty-four. The character had not only graduated from medical school, but worked for the FBI for a year afterwards. She would have to have been at least twenty-seven. When you realize how long it takes to specialize in autopsies, Scully being 28 in the Pilot episode is quite an Improbable Age. Not to mention that she had to train to become an FBI agent and is said to have been a teacher at the FBI academy. She must have been a teen genius or something. note This actually coincides with a case of Improbable Age for Scully as well, which makes this trope even more noticeable. Becoming a forensic pathologist in the US requires a person to graduate from college with an undergraduate degree (4 years), graduate from medical school (another 4 years) and complete a residency (4-5 years), plus a fellowship (1-2 years). The average length of education required is about 13-15 years, plus the two years she'd been working at the FBI. Scully should be in her mid-30's or older at the start of the series, yet she was born in 1964, putting her at 28 when she is assigned to work with Mulder, as the pilot is set in 1992.
Lou Diamond Phillips, Hart Bochner and Bruce Campbell were each finalists for the role of John Doggett.
Johnny Cash was almost a Man In Black in "Jose Chung's 'From Outer Space'"!
Cher agreed to play herself in "The Post-Modern Prometheus" but was unable to due to scheduling conflicts.
Network executives originally wanted someone "taller, leggier, blonder and breastier" to play Scully. They also wanted the role re-cast when Gillian Anderson became pregnant in season two. In both cases, Chris Carter fought against it.
Mitch Pileggi auditioned for some minor roles in season 1, but was not cast. Had he been cast in those, we wouldn't have had him as the awesome AD Skinner.
In "The Pine Bluff Variant", Pennsylvania is misspelled Pennslyvania. Twice.