A deleted scene from Nightmare Cafeteria had Homer regaling Lisa about his dream of eating Milhouse. Regardless, a book from this scene was featured in this segment. As a result of this scene being cut, Homer does not appear in the third segment, something David X. Cohen thought never happened before.
Groundskeeper Willie is killed in all three vignettes while trying to rescue someone. All three happen in the same manner; he gets an ax in his back. In the first vignette he's killed by Homer, the second by Maggie and the third by Principal Skinner.
David Mirkin attempted to put "as much blood and guts" into the episode as he could. This was because Mirkin was disappointed by complaints from Congress regarding the amount of violence in the show and their attempts for it to be censored. He later called it "the most [...] disturbing Halloween show ever". The opening sequence, in which Marge states the episode could not be shown and plays some live action stock footage, was also in reaction to this. Mirkin said he thinks Halloween shows can be "scary as well as fun".
Though this is the last time a warning is used by a Simpsons Family member at the beginning of this episode regarding the disturbing content of this episode, it wouldn't be until 23 years later in The Simpsons: Treehouse of Horror XXVIII (2017) which aired in Season 29 that this segment would be used again due to the disturbing content of the third segment for the latter Halloween episode.
There is a deleted scene on the DVD that takes place during "The Shinning" in which Bart is riding his skateboard through the halls, turns a corner and sees Sherri and Terri who sing "Your father's gonna kill you!". He runs away and turns another corner and sees Patty and Selma who tells him "It's true, ya know".
The various alternative houses that Homer creates via his time-travel escapades: The Flintstones (1960) house The Original McDonalds restaurant which is located in Downey California (and is also the McDonald's Museum at 400 Lee Street, Des Plaines, Ilinois). Shoe house from Mother Goose, Egyptian Sphinx, and an underwater Simpson's house.
The "inside-out gas" that turns the family inside out is a reference to a 1962 radio drama album called "Drop Dead!" by radio performer Arch Oboler. In the segment called "The Dark", a man inhales a gas which turns him inside out.
This episode marked the end of the tradition of featuring humorous tombstones in the title sequence of Halloween episodes. The title sequence of this episode featured a tombstone reading "Amusing Tombstones", which was a sign that the writers could no longer devise ideas to use as humorous tombstone messages. Similar sequences were featured as introductions in all four preceding Treehouse of Horror episodes, but have not been featured since this episode.
The first time Homer travels back in time, he was originally supposed to state "I'm the first non-fictional character to travel backwards through time". The line was later changed from "non-fictional" to "non-Brazilian". Matt Groening was confused as to the reason for the change, since he liked the original so much. In fact, he did not even understand what the new line implied.
Groundskeeper Willie tells Bart not to say Shining, because he could get sued. This seems unlikely, as Stephen King himself has appeared on the show, and other episodes have made reference to other film adaptations, such as Misery (1990) and The Green Mile (1999).
The staff decided against the traditional continuation of featuring wrap-around segments that were featured before each story in the preceding Treehouse of Horror episodes, to allow more time for the main stories.
Matt Groening originally pitched the idea that Homer would travel through time in Time and Punishment. His original idea was that the time-travel would be the result of Homer simply jamming his hand in the toaster, but it was rejected by the other writers.
In a deleted scene involving an alternate Simpsons future, the Simpsons had a teenage son named Roy. Matt Groening said that "somebody from outside the show" originally suggested the idea. The joke was later used as a sub-plot for The Simpsons: The Itchy & Scratchy & Poochie Show (1997), although Roy was a lodger in that episode, rather than a son.
David Mirkin said that Homer's line, "Oh I wish, I wish I hadn't killed that fish", is one of his favorites in the show, and that the alternate future in which the family are rich "breaks [his] heart every time".
The first segment, The Shinning, was inspired by The Shining (1980), and is basically a parody of that film. Stanley Kubrick had been a big influence on David Mirkin, and was "one of the main reason[s] [he] wanted to be a director". Coincidentally, Matt Groening admitted that he had not seen the film and most of the references to the film were entirely lost on him.
In the scene where the Simpsons' house transforms into numerous objects, one of the original designs included the house made entirely of squirrels. The layout artist who designed it worked on the drawings for more than two days, but ultimately it was cut. To ensure their work did not go to waste, some staff members have used the drawings on Christmas cards and other studio-related notices.
In one of the segments, after Groundskeeper Willie is killed by ax, Marge worries if the rug is Scotchgarded. As "Scotch" is one term used to refer to the Scottish (others being "Scots" and "Scottish"), this is able to have two meanings: "Scotchgard" is a product by 3M, used to sometimes protect against stains, whereas "Scotch guard" is able to mean "protection against a Scot", such as Groundskeeper Willie.