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.
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, Pioneer Chicken (the location that was at Hollywood Boulevard and Western), Shoe house from Mother Goose, Egyptian Sphinx, and an underwater Simpson's house.
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.