The Call of the Simpsons: A male character (Homer/Mr. Burns) is mistaken for a mysterious creature that may or may not be real (Bigfoot/an extraterrestrial) and video footage is caught and put on the news about it.
Dog of Death: Mr. Burns goes through a bizarre longevity treatment to cheat death; Homer's "Lousy loveable dog" line is similar to the line, "Lousy, manipulative dog"
Marge on the Lam: Flanders' belongings have the label, "Property of Ned Flanders."
Cape Feare: An elderly character has a strange reaction to not taking or taking the wrong medication: in Cape Feare, Grampa turned into a woman after not taking his medication; in this episode, Jasper turns into a white, hairy monster when he took Wednesday's pills on Friday.
Also: The backroom in Moe's Tavern is used for illegally storing an endangered animal (in Cape Feare, it was pandas; in this episode, it was the killer whale from SeaWorld)
A Star is Burns: A Simpsons episode is crossed over with another show from FOX (though the difference between this one and A Star is Burns is that Matt Groening's name is in the credits in this episode).
Homer Badman: An amateur video proves that Homer was right about something (peeling the gummi Venus off the babysitter's butt/the alien existing)
Bart's Girlfriend: Dr. Hibbert acting negligent towards an elderly patient (leaving his Porsche keys inside Ms. Glick in the former episode, leaving Hans Moleman in the X-ray machine in the latter episode)
Bart Gets Famous: Homer mentions Urkel from the ABC sitcom Family Matters (although, in Bart Gets Famous, Homer wanted to strangle Urkel for being annoying. In this episode, Homer implies that Urkel has a sweet, heavenly voice)
Bart Gets an Elephant: Chief Wiggum refuses to believe an outrageous crime, and shows the same skepticism for a real crime (in Bart Gets an Elephant, it was Stampy roaming through town, followed by the liquor store robbery with an officer down; in The Springfield Files, it was Homer's claim of an alien in the woods, followed by a pyromaniac turning himself in for arson)
Homer and a Simpsons kid (Bart in this episode; Lisa in Bart on the Road) spend the night camping out, complete with Homer roasting multiple marshmallows on a stick over a fire.
Homer mentions that beer is for "daddies" and "kids with fake IDs." Bart had a fake ID in Bart on the Road and he nearly tried beer (but saw how pathetic the patrons of Moe's Tavern looked and refused to drink).
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), making this "the most illegal shot in animation history." The only complaint the writers got was when the man who voices ALF told them that they should have called him up to voice his character.
This is the first episode outside of the "Treehouse of Horror" series to feature Kang and/or Kodos.
Mrs. Glick (the old lady for whom Bart did chores in exchange for comic book money in "Three Men and a Comic Book) is seen at the Springfield Retirement Center, but Three Men and a Comic Book established that, despite her age, she was capable of caring for herself (of course it's entirely possible that since then she had to relocate to the retirement home for one reason or another).
All of Homer's camping equipment when he and Bart are in the woods looking for the alien have labels that read "Property of Ned Flanders."
Leonard Nimoy looks the same way he did when he first appeared in Marge vs. the Monorail (in real life, Nimoy's hair was graying and he had a beard. Why the animators couldn't draw him as he was then is unknown).
In this episode, Bart has a camcorder that was borrowed from Ned Flanders, but in Bart the Lover, Homer tells Flanders that he lost his camcorder (unless that was a different one Flanders bought or Homer was lying).
Marge doesn't have her "Homer is a Dope" shirt on when the alien appears.
Jimbo has a sign that says he needs tickets to Pearl Jam.
Homer says the alien appears every Friday night (like Urkel), which doesn't make sense considering he only saw it once and for all he understood it could have appeared every night or never again.
Mulder's FBI badge has a photo of him wearing a Speedo.
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.
Homer and Santa's Little Helper share the same birthday.
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.
Homer says after seeing Marge's shirt "I'll take two" even though he was just told they sold out. Homer could have forgotten as a result of his many head injuries.
In the crowd scene outside of Homer's door, Lenny Leonard does not have his beard.
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.
The exchange between Smithers and Mr. Burns about whether the former was going to do "something gay" over the weekend was later referenced in Homer vs. Dignity, when Burns while describing Homer's role as prank monkey as more fun than Smithers said that the latter "doesn't even know the meaning of 'gay'."
This episode begins and ends the same way as In Search Of..., the investigative series hosted by Leonard Nimoy.
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. Though 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 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.
After Homer is been 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 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."