References to the television series The X-Files are found throughout the episode:
The title is a reference to the name of series.
Bart writes "The truth is not out there" in the opening scene on the chalkboard. This is a reference to a tagline of the series which is "The truth is out there".
Mulder and Scully are FBI agents from the series, and are voiced by their respective actors.
The Cigarette Smoking Man from the show also appears.
The show's theme song plays whenever the "alien" appears.
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.
When Homer mentions "a movie about a bus that had to speed around the city, keeping its speed over fifty", he is referring to the 1994 action film Speed.
When Homer says, "So, I says, blue M&M, red M&M, they all wind up the same color in the end," he is referring to the introduction of blue M&M's to the lineup of M&M's colors, and the commercials announcing this, as part of the 1995 M&M's Color Campaign, a contest in which blue, purple, or pink would be selected as the new color.
After Homer is been examined by Scully and Mulder, a view of Moe's Tavern is shown with a brief description, after which the text "ALL WORK AND NO PLAY MAKES JACK A DULL BOY" text is repeatedly typed on-screen. This references a famous scene from the 1980 film The Shining by Stanley Kubrick.
Mulder mentions the unsolved mysteries of Unsolved Mysteries, a show premised on mysterious cases that remained unsolved.
Psycho: The busload of musicians that Homer encounters while in the woods play the music from the shower scene.
The Budweiser Frogs appear in the lake near the woods before getting eaten by a gator that says "Coors!" which is the name of another beer company.
Leonard Nimoy's narration of the story references the TV show In Search Of..., which he hosted.
Milhouse is seen playing an arcade game based on Kevin Costner's movie Waterworld. The game is over only a few seconds after it starts, and he calls the game a ripoff. This is a reference to the movie being extensively hyped, but turning out to be mediocre.
Grampa calls a tortoise a turtle. However, this may be due to his senility, not a goof.
After the scenes with the T-shirts, when the alien arrives, Marge's "Homer is a dope" shirt disappears and she has her normal dress on.
At the kitchen table, when Homer talks about being mocked on his own birthday, they're eating breakfast. But when Marge, Lisa, Bart and Maggie all go to pet Santa's Little Helper, the breakfast has vanished.
When the 'alien' is seen on the news, it is shown on the film Bart made coming out of the trees, but earlier on, when the alien came out of the woods, Bart is seen not holding his video camera.
Homer's only been working at Springfield Nuclear Power Plant since 1980. The tape of Homer working appears to be from the mid to late 70s. Also, Homer's only been a safety technician in sector 7-G since 1990.
Homer tells Wiggum that the alien appears every Friday night, even though he saw it only once.
The writing on Moe's breathalizer changes between scenes.
Lisa's "Junior Skeptic" magazine appears out of thin air.
Despite having the funds to hire the best medical care, Burns has Dr. Nick on his medical staff.
Apu, a vegetarian, is seen standing in line at a hot dog stand. However, it's possible that the stand also sells vegetarian hot dogs.
Mr. Burns has been seen at night several times (both before and after this episode) without glowing.
When Mulder talks about the inevitability of the existence of aliens, he briefly has yellow eyes.
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.
