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.
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.
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.
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".
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 Treehouse of Horror XXVIII 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.
At the beginning of the third spoof, Bart walks by the detention room and Wendell is trapped in there. Seconds later he goes to the cafeteria for detention and Wendell is now sitting at the table behind Bart.
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 and The Green Mile.