When Homer says "a movie about a bus that had to speed around the city, keeping its speed over fifty" he is referring to the 1994 film Speed.
Much of the episode contains references to TV show The X-Files. Mulder and Scully are FBI agents from the series, and are voiced by their actors. The Cigarette Smoking Man from the show also appears. The show's theme song plays when the 'alien' appears, Mark Snow should've been credited for composing the theme song. Also the photo of Mulder in a speedo shown in his FBI badge is a reference to an episode of the series where Mulder is shown wearing one.
J. Edgar Hoover (the first and longest serving director of the FBI) is wearing a dress in the photo in the X-files office. In his biography Official and Confidential: The Secret Life of J. Edgar Hoover (1993), journalist Anthony Summers quoted "society divorcee" Susan Rosenstiel as claiming to have seen Hoover engaging in cross-dressing in the 1950s, at all-male parties. Although this has never been corroborated and most historians say it has been debunked.
Milhouse is shown playing "Kevin Costner's Waterworld" at the arcade. The game is shown to be both expensive (costing 40 quarters/$10 to play) and underwhelming (with game over occurring after the player walks a single step). This references the large budget for the film (which prior to Titanic was the most expensive film produced) and its weak critical reception and box-office performance.
Coincidentally, several video game adaptations of Waterworld existed that were similarly panned, with the Virtual Boy version in particular being considered the worst entry for the system.
The Line up - This is considered the most illegal scene in Simpsons' history
After Homer is being examined by Scully and Mulder, a view on Moe's Tavern is shown with brief description, after which "ALL WORK AND NO PLAY MAKES JACK A DULL BOY" text is repeatedly written on screen. This refers to famous scene from The Shining by Stanley Kubrick.
The bus of musicians that Homer encounters while in the woods play the music from the shower scene in the horror movie Psycho.
The Budweiser Frogs appear in the lake near the woods before getting eaten by a gator that says "Coors!"
"Keep watching the skies!" is the last sentence in "The Thing from Another World."
Trivia[]
According to DVD commentary, none of the writers got permission to use any of the aliens in the police line-up (except for Kang/Kodos, which is the show's creation. and, retroactively, Chewbacca, since Disney now owns both Lucasfilms and FOX), making this "the most illegal shot in animation history." The only complaint the writers got was when Paul Fusco, the man who voices ALF, told them that they should have called him up to voice his character rather than use the regular staff.
This is the first episode outside of the "Treehouse of Horror" series to feature Kang and/or Kodos.
According to DVD commentary, the ending was originally supposed to keep the alien's identity a mystery, implying that Homer really did see an alien.
A lie detector violently reacts to someone lying (the polygraph machine beeps after Moe's repeated lies about what he plans to do after the test/the polygraph machine blows up after Homer answers "yes" to "Do you understand?")
"Cape Feare": An elderly character has an adverse reaction to medication (Grampa Simpson turns into a woman without his meds/Jasper taking his Wednesday medication on Friday turns him into a hairy monster).
"El Viaje Misterioso de Nuestro Jomer": Homer has a strange encounter that everyone (including his wife) dismisses as either crazy or the product of being drunk.
"Homer Badman": Marge doesn't come to Homer's defense over something (the sexual harassment claims against him/the alien existing)
"Radio Bart", "Duffless", "Much Apu About Nothing", and "Bart on the Road": Fake IDs are mentioned (Bart laments that being stuck in the well means he'll never get to use a fake ID/Homer as a teenager had a fake ID so he can buy beer/Kearney has a fake ID, but Apu is so depressed about being deported that he doesn't notice or care/Bart creates a fake ID while spending the day at the DMV with Patty and Selma/Homer tells Bart that beer is "for daddies and kids with fake IDs").
"Radio Bart": Springfield has an outdoor carnival dedicated to something bizarre (Timmy O'Toole trapped in the well/the alien appearing).
"Mr. Plow", "Krusty Gets Kancelled", "Cape Feare", "Bart of Darkness", and "Bart's Girlfriend": Self-depreciating jokes about the FOX network (Homer's line, "It may be on a lousy channel, but The Simpsons are on TV"/Krusty hates his half-brother Luke Perry because he's on a popular FOX show/Lisa's line, "The FOX network has sunk to a new low" after seeing Up Late with McBain/Homer tries to cover up calling Maude a fox by asking "What's on FOX tonight? Something ribald, no doubt."/Bart recounts the time he watched an episode of Martin, which, at the time, was on the FOX network/Homer suggests that he and Bart fake the footage of the alien and sell it to FOX, Bart says FOX will buy anything, and Homer reminds Bart that they make quality programming, before the two of them laugh at the ridiculous claim).
"When Flanders Failed", "Lisa's First Word", and "Marge on the Lam": Everything Homer has is "Property of Ned Flanders" (the furniture Ned had to sell because of his failing left-handed store/the TV tray Homer asked for when he, Marge, and Bart moved in/the power sander that Ruth wanted to borrow/the camping gear).
"Bart Gets an Elephant": Chief Wiggum ignores both a crime that seems fake (the elephant rampaging through town/Homer seeing the alien) and a real crime (a liquor store robbery with an officer down/a pyromaniac turning himself in for arson).
"Brush With Greatness": A character voiced by Dan Castellaneta (Krusty/Homer) shuts down an interview after someone asks a personal question (the Krusty mayonnaise being tainted/Flanders wondering if Homer stole his weather vane).
"Bart Gets Famous": Homer and Urkel (Homer angrily says that he'd like to strangle Urkel because of how annoying he is/Homer thinks Urkel has a sweet, heavenly voice during his report on his alien sighting).
Goofs[]
Marge doesn't have her "Homer is a Dope" shirt on when the alien appears.
Homer says the alien appears every Friday night (like Urkel), which doesn't make sense considering he only saw it once. That's more or less a joke on the character Steve Urkel from Family Matters, judging by the fact that Homer thinks Urkel has a sweet, heavenly voice. Also, "Bart Gets Famous" reveals that Homer hates Urkel because of how annoying he is.
White Duff labeling
The Duff Beer bottles at Moe's Tavern have white labels instead of the usual red ones.
Mulder with yellow eyes
When Mr. Burns is getting his treatment, his eyes grow wide when he gets his eye drops, but his eyes grow wide when he is injected with his medicine.
When Mulder talks about the inevitability of the existence of aliens, he briefly has yellow eyes.
Lenny without a beard
Homer says after seeing Marge's shirt "I'll take two" even though he was just told they sold out.
In the crowd scene outside of Homer's door, Lenny Leonard does not have his beard.
Kent (back row) has gray hair
When Homer is at Moe's with Mulder and Scully, the beer bottle he's holding sounds mostly empty when shaken, but when he slams the beer down it fizzes out an amount more in line with a full bottle.
In the final scene, Kent Brockman has gray hair instead of his usual white hair.
Leonard Nimoy looks the same way he did when he first appeared in "Marge vs. the Monorail" (in real life, at this point, Nimoy's hair was graying and he had a beard).
When we see the "alien" completely glowing green, he appears to be completely bald even on the sides, and has a very small nose and no visible teeth in his small mouth. But then Lisa shines her flashlight on the "alien" revealing it to be Mr. Burns, who suddenly has his hair on the sides and his distinct long pointy nose and tooth-filled mouth.
Dan Castellaneta's voice for the pyromaniac who turned himself in for arson slips into sounding like Homer in the last half of his line, "I just torched a building downtown and I'm afraid I'm going to do it again!"
