- To start, there's "Home", one of the most infamous episodes of the whole show, and the only one that was never shown on Fox again for several years after its premiere (it can now be seen on DVD and streaming). A Mundanger that starts with an inbred family burying a hideously deformed baby outside their farmhouse and gets worse from then on, it's an episode that would likely push an R-rating as a film. The rest of the story features moments like a family being beaten to death with baseball bats, impromptu death traps, and the reveal that the Peacock family sons keep their limbless mother under the bed and try to impregnate her—in fact, the eldest brother is the father of the other two, and all three are the father of the dead baby. How it got past the censors with just a viewer discretion warning is still a mystery worthy of a Mulder and Scully investigation.
- In the second season episode "Blood", Mulder is sprayed with an experimental chemical that is shown to cause subliminal effects to its target and sees an attractive woman on TV advertising a fitness center. The words on her shirt? "DO IT."
- In second season episode "Aubrey":
Mulder: Well, I'd like to know why this police woman would suddenly drive her car into a field the size of Rhode Island and for no rhyme or reason, dig up the bones of a man who's been missing for 50 years. I mean unless there was a neon sign saying 'Dig Here'.Scully: I guess that's why we're going to Aubrey.Mulder: Yes, and also, I've always been intrigued by women named BJ.
- Deep Throat. Of course, the name is a reference to Woodward and Bernstein's famous informant, but it's pretty incredible that they were able to say that phrase — on network television — so many times given the porn film and sexual act that it really referred to.
- The title of the third season episode "War of the Coprophages" could be a clever way of saying "war of the shit-eaters". Could also reference Mulder and Scully's verbal conflict during the episode.
- The tenth episode of the 5th season is named "Chinga", like the doll that stars the episode, which is Mexican Spanish for "f**k" (in sexual context). Maybe it's because of that that the episode was renamed "Bunghoney" in the UK.
- In the 3rd season episode "Teso Dos Bichos", "bichos" is an euphemism for "testicles" ("balls") in Colombia and Argentina. One member from the crew joked that this "controversy" would be good for ratings.
- In the 7th season episode "Signs and Wonders," the agents investigate a church that practices snake-handling. Scully says snake handling is something she never learned in Sunday school, and Mulder replies, more crassly than usual, "funny, I knew Catholic schoolgirls who were experts at it." If that went over your head, he's referring to handjobs.
- In Season 7's "Je Souhaite", Mulder and Scully are able to dance around the cause of the death of the female genie's previous master, apparently he wished for a Gag Penis, which caused his death, using terms like "extreme priapic condition".
- In Season 1's "Fire"
Scully: Yeah, I noticed how you couldn't drop everything fast enough in order to help her out.Mulder: I was merely extending her a professional courtesy.Scully: Oh, is that what you were extending?
- Mulder in "Chinga" is supposedly watching a tape of the "World's Deadliest Swarms", though the moaning noises and the viewer knowing his favorite form of entertainment would suggest otherwise.
- In Season 11 episode "This", after Mulder is able to successfully take down one of the Mooks that have been hassling them during the entire episode while his hands are cuffed behind his back (keep in mind that at this point, they definitely have had a romantic relationship in the past):
Scully: (unlocking the handcuffs) How is it that you're able to operate so well with your hands cuffed behind your back?Mulder: As if you didn't know.
Radar / The X-Files
The truth is out there... but so are sexual innuendos, dark and horrifying moments, and Squick that could push the boundaries of network TV.