The newspaper article Mulder reads at the end of the film (titled "Fatal Hanta Virus Outbreak in Northern Texas Reported Contained") was written by reporter Howard Dimsdale. The real Howard Dimsdale taught X-Files writers Frank Spotnitz and John Shiban at the American Film Institute, and was "black listed" during the McCarthy era. See the in-jokes for season 5's episode "Travelers" for further references to Howard Dimsdale.
The Well-Manicured Man's car has an interesting license plate. It reads "LA365" -- which many have taken to mean that the crew for the movie wanted the show to move from Vancouver to LA and film there all year (365 days a year, that is).
When all of the bathrooms are occupied, Mulder finds relief outside in the alley -- under a poster for 1996's hit movie "Independence Day". While this is more of a regular joke than an inside-joke, it is worth mentioning here not only because of the obvious alien tie-in, but also because the X-Files television show was mentioned in the movie "In dependance Day" itself (see the Outside-Inside Jokes page for further information).
As the movie closes, Cancerman and Strughold continue their colonization plans in Foum Tataouine, Tunsia. While Fouh Tataouine is not a figment of Carter's imagination (translation: it is a real place in Tunsia) Newsweek reports that Fouh Tataouine is a reference to 20th Century Fox's other mega Sci-Fi movie, Star Wars (Tatooine was Luke Skywalker's home).
I really don't have confirmation on this one, but the first agent that runs into the vending room after the door is broken down looks an awful lot like Jason Beghe. One of David Duchovny's best friends, Beghe also appeared in the season one episode "Darkness Falls" and was rumored to have a small role in the movie.
The agent "on guard" outside Mulder's hospital room is the assistant director.
Former LAPD bomb squad officer Herb Williams and former FBI agent Will Heaton acted as advisors for the bomb sequence -- and appeared in the movie as agents in a scene with Scully.
In the scene where Scully collapses in Mulder's hallway due to that nasty bee, she just happens to lie down on honey-comb-patterned linoleum.
In keeping with the bee-theme, it is worth mentioning that Scully quit because she was going to be transferred to Salt Lake City, Utah -- and that Utah is also known as the "Bee-Hive" State (the Bee-Hive being the symbol for industry on their state flag).
Conrad Strughold was named for the real Strughold, a Nazi scientist who conducted experiments on prisoners during World War II. The U.S. government secretly brought Strughold over after the war to work on the space program. It is also worth mentioning that in season 3's "Paper Clip", Mulder & Scully discover "lots and lots of files" at the Strughold Mining Company.
Stevie is named after one of Carter's boyhood friends. Carter says that he and the real Stevie used to dig holes a lot, just like in the movie.
Dr. Alvin Kurtzweil is also based on a real person, a doctor who supposedly died under suspicious circumstances.
Kurtzweil's beliefs may be modeled after Milton William Cooper, a real-life conspiracy theorist who has written conspiracy books similar to those seen in Kurtzweil's apartment. One of Cooper's books is titled "The Secret Government", and he was the first to suggest that FEMA would take over the U.S. Government, saying such things as "it will happen on a holiday, when patriots are away from their homes". The phrase "silent weapons for quite wars" also appears in his work. It is also worth noting that the name "COOPER" is on the back of the "fake" ambulance that Scully is loaded into.
Those "Special" Numbers:
619 - the number on the "Office of Professional Review" door (where Scully is interrogated by the Assistant Directors). 06/19 is the date that the movie opened.
11:21 - the time Mulder goes to the Dallas Field Office, where Scully joins him and analyses the fossils. 11/21 is the birthdate of Chris Carter's wife.
1121 - a number on one of the domes in Antarctica. 11/21 is the birthdate of Chris Carter's wife.
0619 - a number on one of the domes in Antarctica. 06/19 is the date that the movie opened.
1013! - when Mulder is trying to convince Scully that he is indeed locked in with a bomb, the first countdown-time number Mulder recites to her is 13:56 (Chris Carter's birthdate day & year -- 10/13/56)
1013???? - the last 4 digits of Scully's cellular phone number are 0113 (at least that's what I see - and I have lots of practice looking for this sort of thing). Many people, including the reporter from Newsweek, claim that her number is actually 1013 (Chris Carter's birthdate).
10:13 - The "hidden" track on The X-Files: The Album (the soundtrack album - not Mark Snow's score) takes place 10 minutes and 13 seconds into the last track. The "hidden" track is a spoken word piece by creator Chris Carter, who explains some of the Syndicate's history and motivation
"Blackwood" is the name of the Texas town where the "mutated" life-form first rears its ugly head -- where Stevie and the 4 Firemen are infected.
"Blackwood" could be a reference to an "interesting" magazine that was published in the 1800's called "Blackwood's Magazine", or "Blackwood's Edinburgh Magazine". It was known for printing horror and other outrageous stories, most of which were written as if they were true. Edgar Allen Poe wrote a few short stories referencing this magazine, one called "How to Write a Blackwood Article" and "Loss of Breath -- A Tale Neither In Nor Out of 'Blackwood'" (he also listed the fictitious author of this story as Mr. Blackwood Blackwood). Even if this isn't the real reason for the title, it is still kinda cool!
"Blackwood" is also a term used in bridge. Apparently, it is a method used to find out how many aces or kings your opponent has.
Due to creator Chris Carter's desire for secrecy, the X-Files movie was filmed under a code-name. Instead of calling it "The X-Files - the Movie", it was called "Blackwood". Just where did the code-name "Blackwood" come from?
Check out the He Said, She Said and the X-Files Lists & Statistics pages for more movie references.
Check out Fight the Future Script Differences for various cut scenes and differences from the script to the screen.
For boatloads of information on the movie, check out the Official X-Files Movie Page.