This list of in-jokes is almost entirely based on Laura Witte's In-jokes list, I made only some little updates, mainly "retreads". Please visit also her site.

• Being the first episode of Season 9, now would be a good time to mention the fan-reference in the new Season 9 credits. During the credits sequence there is a flash of a document containing the names of many online X-Philes (as well as some anagrams of X-Files characters -- for example "Deform Redux" is Fox Mulder) under the heading "FBI Contacts, Witnesses and Contributors" (the heading on the advance screening copy included the line "*(Possible Hybrids)").
• This episode contains some excellent references to the now-cancelled "Lone Gunmen" series, including both Frohike and Byers making references to being "unemployed". Langly is wearing the blue face paint from the final cliffhanger episode.
• Assistant Director Brad Follmer is named after Chris Carter's Executive Assistant.
• The worker at the Greater Maryland Water Reclamation Facility is named after Roland McFarland, the FOX network's Vice President of Broadcast Standards.
• Writer Steve Maeda's name was listed on Doggett's list of soldier friends.
• Ryan Bracker and Shannon McMahon are names that Chris Carter made up, although they do have some secret significance.

• Not an in-joke, but this episode was dedicated "In loving memory of Chad Keller - October 8, 1971 - September 11, 2001".
• The tagline changes to "Nothing Important Happened Today".

• The hospital guard reads "American Ronin" magazine, which appeared in season three's "Pusher".
• "The Inverted Cross", a symbol also known by the name "St. Peter’s Cross", originated as a Christian symbol that represents the great humility of St. Peter. At his own request, the disciple was crucified head downward because he felt unworthy to die as Christ had died. In modern times, this symbol has been adopted by Satanists to represent their rejection of Christianity.
• Writer/Director Frank Spotnitz's wife, Melissa, appears as one of the cadets in Scully's Quantico class.

• A dog in the script named Happy is named after Gillian Anderson's dog.
• The doctor who works at the mental institution is named Sackheim for the X-Files director (though the doctor is female).

• Not an in-joke, but this episode was dedicated "In Loving Memory of Ricky Loyd Arreguin - January 24th, 1985 - September 13th, 2001".
• The tagline "The Truth Is Out There" is mirrored, which is in keeping with the entire teaser. To emphasize the episode's theme of parallel universes, the film in the teaser was flopped to show a mirror image of the action captured by the television camera. Characters who are right-handed appeared to be left-handed, and entrances that were on the left are depicted on the right. Special attention was paid to the written words on badges and signs. Each word was carefully written backwards on the set, with certain letters turned around in the same way the word "ambulance" appears on emergency vehicles.
• The many worlds, or "multiverse" theory, a radical interpretation of quantum mechanics, lays out the idea that we all have identical counterparts in a countless number of other universes. In 1967, American physicist Hugh Everett first suggested the theory to make sense of the random behavior of subatomic particles, believing that these particles occupied more than one position at the same time. According to Everett, if this was true for subatomic particles, then it is true for everything else. Intrestingly, a movie called "The One" made by former X-Files authors Glen Morgan and James Wong alse deals with multiverse.
• A Spinal Cord Injury (SCI) is damage to the spinal cord that results in a loss of function such as mobility or sensation of touch. An SCI restricts the ability of the brain to transmit nerve impulses to the body and inhibits it from receiving them in return. It is estimated that approximately 11,000 new cases of SCI are found each year in the United States. The primary causes of SCI are motor vehicle crashes, acts of violence (primarily gunshot wounds), falls, and recreational sporting activities.
• Doggett's use of his pinkie finger to communicate is inspired by The Diving Bell and the Butterfly, the moving autobiographical story of Jean-Dominique Bauby. The author was struck with a rare disease called "locked-in syndrome", in which a patient suffers nearly complete motor paralysis, rendering him unable to communicate except by blinking his eyes. It was in this manner that Bauby laboriously conveyed his thoughts and emotions about being a prisoner inside his own body.
• Monica Reyes' new Georgetown apartment address of 67 Bennett Avenue was actually Rod Serling's home address in Binghamton, NY. The address was also used in "They're Tearing Down Tim Riley's Bar", Serling's Emmy-nominated episode of Night Gallery.
• Reyes' apartment number is 6, and was chosen because it was Patrick McGoohan's number in the 1967 television series, The Prisoner.

• The aggressive flies in this episode were inspired by the actual habits of the blow fly, especially the Australian species, the Musca vetustissima Walker. While many species of blow fly are found worldwide, these stout insects of the land down under are particularly aggressive in their hunt for protein excreted by both humans and animals. The flies search for protein contained in saliva, sweat, mucus and blood, and they will attempt to get at it through any open orifice they can find. Fortunately, these flies are more of an irritating nuisance than a physical danger to their chosen victims.
• Roger Keith "Syd" Barrett was the founder and original singer, songwriter, and lead guitarist of Pink Floyd. While the band's first album was sitting high on the UK charts, the band was facing a personnel crisis: Syd Barrett was using so much LSD that he became very unstable, often staring into space while the rest of the band performed. He missed recording sessions and shows, and even disappeared for days at a time. In January of 1968, the band brought in David Gilmour, who had gained reputation as a skillful guitarist, to cover for Barrett on stage. After only a few shows, it became apparent that Barrett could no longer perform at all. On the way to a show one night, the band simply did not pick him up, and he was officially fired a few months later. Yet Barrett and Pink Floyd remained friends. After a period of hibernation, Barrett re-emerged in 1970 with a pair of albums that attracted little attention at the time. It is theorized that these records are a glimpse into a creative psyche gone awry after too much fame and too many drugs at such an early age. With increasing psychological problems, Barrett withdrew into near-total reclusion. He never released any more material, and rarely appears in public, let alone to play music. Yet his albums today still attract a cult audience.

• Mrs. Doggett is played by Barbara Patrick, Robert Patrick's wife.
• "Hollis Rice" was named for writer Vince Gilligan's girlfriend, Holly Rice.

• The tagline changes to "They're Watching".
• 925 - Scully's e-mail, queequeg0925@hotmail.com (9/25/94 is the birthdate of Gillian Anderson's daughter, Piper).
• The email addresses for Mulder and Scully in the episode are real, working accounts set up by Ten Thirteen Productions.
• The classical music in the episode is Peter Ilyich Tchaikovsky’s "The Seasons: Barcarolle", which was arranged and performed by Richard Grayson.
• Retreads: Terrance Quinn (Shadow Man) appeared as Lieutenant Brian Tillman [Aubrey] and as Special Agent Darius Michaud [The Movie] (both of these under name Terry O'Quinn).

• The character Duke Tomasick is named after the show's Construction Coordinator.
• Retreads: Rick Garcia (Reporter #1) was News Anchor [Three of a Kind]. Leah Sanders (Reporter #3) was Reporter #1 [Theef].

• Retreads: Tracey Ellis (Audrey Pauley) was Lucy Householder [Oubliette].

• The tagline changes to "Dio Ti Ama", which is Italian for "God Loves You".
• The Executive Producer credit was changed to "Produttore Esecutivo".
• Carter interspersed playing card terminology throughout his script. The term "fifth street" is from flop games, and refers to the final round of betting and the fifth community card on the board. In stud games, "fifth street" is the fifth card dealt to each player and the third betting round (on the third upcard).
• In parking garage scene where Scully and Reyes play checkers, all of the automobiles are classic cars.
• To fit in with his numerology theme, Carter wanted three Italian girls to open up the scene at the San Generro Feast. He asked Ten Thirteen assistant Sandra Tripicchio and her two sisters, Cara and Christine to work as extras in the show. The Tripicchios are triplets.
• Props department crew member Tighe Barry plays a homeless man in the San Generro Feast scene.
• Former Ten Thirteen Production Assistant Angelo Vacco appears as two characters in the episode. He plays the bartender as well as Guido, the guy with the girlfriend at the San Generro Feast.
• Retreads: Angelo Vacco (Bartender and Guido) was Angelo Garza [F. Emasculata], Door man [Talitha Cumi] and Kevin [Milagro].

• There's a character named "John Gillnitz" in this episode. The name is a combination of the 3 staff writers (John Shiban, Vince Gilligan, and Frank Spotnitz).
• The role of Speaker is played by Thomas Schnauz, who wrote episodes "Lord of the Flies" and "Scary Monsters".
• Retreads: Timothy Landfield (Professor Douglas Houghton) was Scientist/Cobra [En Ami].

• Jared Poe, who plays Rudolph Hayes, was a trainee on the Season 9 writing staff through the Writers’ Guild of America minority program. Jared had wanted to experience the audition process, and ended up landing the lead guest star role because he was such a good actor.

• 1121 - time when we see Doggett do his push-ups
• Retreads: Chris Bradley Owens (The Breather) appeared earlier as Young Cigarette-Smoking Man [Musings of a Cigarette-Smoking Man, Demons, Two Fathers], Mutato [The Post-Modern Prometheus], Mulder's Dad [Dreamland II] and mainly as Agent Jeffrey Spender [Seasons 5, 6, The Truth].

• The date mentioned on the videotape is April 4th, 1970. April 4th is the birthday of writer Vince Gilligan's girlfriend, Holly.
• The main character in this episode has changed in name to "Oliver" in reference to the cousin who appeared in the final episodes of "The Brady Bunch".
• Retreads: Arlene Pileggi (Arlene), who happens to be Mitch Pileggi's wife and Gillian's stand-in, appeared in several episodes: as Skinnner's Secretary/Assistant [Bad Blood, Triangle, S.R. 819, Monday, The Sixth Extinction II: Amor Fati, This Is Not Happening, DeadAlive], Woman Who Looks Like Scully [Fight Club] and as 1st Woman Party-Goer [Essence].

• 1121 - time of the cut to USMC Base Brig
• December 22, 2012 is apparently where the Mayan (Aztec) calendar ends.
• Retreads: Christopher Stapleton (???) was Pilot [Dreamland].