During Marge's introduction, a black-and-white movie clip appears which is ostensibly from a movie called 200 Miles to Oregon. No such movie by that title exists, but it might be a reference to the original 3:10 to Yuma, in which Glenn Ford starred as Ben Wade.
Bart's introduction (where his voice appears as waves on an oscilloscope) is a parody of the Control Voice's introduction in the 1960s TV series The Outer Limits.
The Shining - Referenced in the title and parodied throughout the segment.
Maggie spells "REDRUM" with her blocks when Homer tries to watch the TV.
Analogous to Jack Torrance endlessly typing "All work and no play makes Jack a dull boy," Homer writes "No TV and no beer make Homer go crazy" all over the walls. The only thing Homer types is "Feelin' fine," which briefly reassures Marge, until a lightning flash reveals the writing on the walls.
When Groundskeeper Willie says to Bart that he has got the Shinning, Bart says "You mean Shining?!" to which Groundskeeper Willie says "Ssh! Do you want to get sued?!"
Homer does the "Heeeere's Johnny!" scene, but he breaks into the wrong room, which is vacant. He then breaks into another room announcing himself as David Letterman, only to discover that Grampa has finally arrived. The third and final time, he finds the right room and announced himself as several guests on 60 Minutes.
When Marge discovers that Homer has written 'No TV and no beer make Homer go crazy' all over the walls, Homer bursts through a door and scares her. In The Shining, Jack sneaks up on Wendy and asks her what she thinks of his 'book'. In the film it is written as : "All work and no play makes Jack a dull boy".
Jurassic Park - When Homer first arrives in the past, he says, "I've gone back to the time when dinosaurs weren't just confined to zoos!" Also, the theme song plays for a moment.
A Sound of Thunder - The idea that Homer causes significant alterations to the future by killing a mosquito is a parody of A Sound of Thunder in which a hunter goes back in time to hunt dinosaurs. The hunter kills a butterfly by accident only to find that this alters the future the hunter returns to.
Ned Flanders being the absolute lord and master of the world, similar to Big Brother in George Orwell's 1984.
The Flintstones - The Simpsons' house momentarily changes to the house owned by the Flintstones.
The song the inside-out Simpsons and Groundskeeper Willie sing and dance to is a parody of "One" from A Chorus Line. It was also played at the end of "The Shinning."
Danny Elfman is credited as "Danny Skellingelfman. This is an obvious reference to The Nightmare Before Christmas' Jack Skellington. Also he wrote the music and he did Jack's singing voice for the film"
Dan Castellaneta is credited as "Ro-Dan Castellaneta from the movie Rodan."
Dave Sacks is credited as "Dave 'The Friendly Ghost' Sacks from Casper The Friendly Ghost."
Pamela Hayden is credited as "Pamela 'Poltergeist' Hayden from the movie Poltergeist."
Hank Azaria is credited as "The Shaws-hank Azaria from The Shawshank Redemption."
Before Mr. Burns and Smithers leave for the winter, Smithers suggests to Burns that cutting off the cable television and beer supply might have been the reason that the previous caretakers went insane and murdered their families. Burns then says that owes Smithers a Coke if everyone gets slaughtered, which he also says in "Treehouse of Horror II" in the scene where him and Smithers are returning Homer's brain to his body.
A deleted scene features Bart encountering Sherri and Terri as the ghosts of the previous caretaker's daughters. Bart is skateboarding in the halls, turns a corner, and sees Sherri and Terri, who sing, "Your daddyyyy's going to kill youuuu." Bart then skates down another hall and sees Patty and Selma, who tell him, "They're right, y'know." The scene also shows Dracula, the Mummy, the Werewolf, Freddy Krueger, Pinhead, and Jason Voorhees coming out of the rooms and watching Bart.
If you look at the upper-right hand side of the crowded detention, you can cleary see Lisa, yet the reason is unknown. Lisa being sent to detention in Treehouse of Horror XX in Dial 'M' for Murder became a plot for that section.
When the machine picks up the Simpsons house, to take it to the 'Re-Neducation Center', the garage is on the wrong side of the house. It is on the correct side in the following shots of Homer returning.
When Marge, Bart and Lisa are speaking with Ned, Marge's pearls are white instead of red.