For Mulder's rambling about the truth, the crew just left the microphone on and let David Duchovny ramble about whatever he wanted. He went on for two hours before he ran out of steam.
"Skeptic Magazine" actually created "Junior Skeptic Magazine" after seeing Lisa reading it.
The aliens seen in the FBI lineup are Marvin the Martian, Gort from The Day the Earth Stood Still (1951), Chewbacca, ALF (1986), and either Kang or Kodos. Producer Mike Reiss jokingly referred to the scene as the "most illegal shot" in the history of the show. The only complaint the writers got was when voice actor Paul Fusco told them that they should have called him up to reprise his ALF (1986) voice.
This is the first episode outside of the "Treehouse of Horror" series to feature Kang and/or Kodos.
When Mulder and Scully flash their badges at Homer the first time, Mulder's wallet has a picture of him posing in a Speedo, a spoof of his iconic scene from Duane Barry (1994).