Blaine (talking about Scully and Mulder): One of them was disguised as a woman, but wasn't pulling it off. Like, her hair was red, but it was a little too red, y'know? And the other one, the tall, lanky one, his face was so blank and expressionless. He didn't even seem human. I think he was a mandroid.
Absurdism: One of the best examples of this philosophy in recent TV, this episode actually has a serious message under all the comedy: it's about the conflict between the innate human desire to make connections with other and the fact that we are ultimately isolated by the subjective nature of our own perceptions.
Lt. Schaefer: Have you ever flown a flying saucer? Afterwards, sex seems trite.
Celebrity Paradox: Zig-Zagged. Jeopardy!'s Alex Trebek and wrestler/future governor Jesse "The Body" Ventura appeared in the roles of The Men in Black. The man in black played by Ventura was described as "creepy," while the one played by Trebek just "looked like Alex Trebek," which made those reporting them seem all the more crazy.
No Celebrities Were Harmed: Chung is largely based on Truman Capote, with his research trip to Klass County and boasting about creating a "new literary genre" of "non-fiction science fiction" being pretty obvious parallels to the making of In Cold Blood. He's also (like his actor Charles Nelson Reilly) very obviously gay, though this is never directly commented upon.
Klass County was named after Philip Klass, a prominent UFO skeptic.
Detective Manners was based on show director Kim "Bleeping" Manners, who did curse like that in real life.
Prison Rape: Mulder tells Harold that he's likely to experience this. The threat is gentler than you might expect because Mulder is sure that Harold is innocent of taking advantage of Chrissy, and is also trying to get the truth about the UFO.
Room Full of Crazy: The Conspiracy Theorist who believes in aliens and who wants to be abducted in "Jose Chung's From Outer Space" has a corner in his room which is a nice foil to Mulder's office. He even has a similar poster but the message reads "I believe".