Roger Meyers, Sr. being cryogenically frozen is a reference to the myth that Walt Disney's head was similarly frozen.
Itchy's former name of "Itchy the Lucky Mouse" was a reference to the prototype to Disney's mascot Oswald the Lucky Rabbit, and in fact, the backstory regarding Chester Lampwick, Meyers Sr., and Itchy's creation was a reference to a similar incident regarding Walt Disney, Ub Iwerks, and then-Universal Studios head Charles Mintz, where Disney and Iwerks initially created Oswald, but were legally forced to give exclusive ownership of the character to Universal Studios when they left, which ultimately resulted in them creating Mickey Mouse, the actual mascot for what would eventually become the Walt Disney Company. In this case, however, Meyers, Sr. was closer to Mintz while Lampwick was similar to Disney/Iwerks.
The Manhattan Madness cartoon in "The Day the Violence Died" is based on very early animated cartoons such as Gertie the Dinosaur.
The "Amendment To Be" segment is a parody of the educational show Schoolhouse Rock, and more specifically "I'm Just a Bill", and refers to the Flag Desecration Amendment. Jack Sheldon, who sang the original song in "I'm Just a Bill", voices the song in the "Amendment to Be" segment.
The cartoon "Itchy and Scratchy Meets Fritz The Cat" is a reference to the 1972 animated film Fritz the Cat, which was the first X-rated animated film and became notorious for showing drug use and sexual situations openly.
The first Itchy & Scratchy cartoon, "Steamboat Itchy"(which originally appeared in Itchy & Scratchy: The Movie) is a reference to Steamboat Willie, one of the first Mickey Mouse cartoons. Joseph P. Kennedy, father of former United States President John F. Kennedy, is listed as one of the cartoon's producers.
Lampwick references Alan Becker's animation "Animation vs Animator".
A slogan to Itchy and Scratchy marathon is "The 48-hour Itchy & Scratchy Diamond Jubilee Marathon: Celebrating 75 years of rib-tickling brutality and hilarious atrocities."
Apu is arrested for public indecency. We also find out in that same sequence that Krusty had an estranged wife which would be the main story for the episode Insane Clown Poppy.
Hosting the parade with Suzanne Somers is famed news anchor and commentator David Brinkley.
The scene where Lester skateboards past the Simpsons house and stares at Bart is a reference to 5 episodes earlier when Bart first skateboards past the house of George Bush
As pointed out in special features, the film case changes color from black to pink after it is tossed in the garbage.
During the cut to the basement (after the scene where Bart first sneaks into the house and says "The coast is clear"), Bart's image seems to jump from a point at the top of the basement stairs to the middle (without any animation in between) when telling Chester that there is where he is going to sleep.
The Empire State Building can be seen in Manhattan Madness, even though it opened in 1931, whereas Manhattan Madness was created 22 years earlier.
The fact that this episode is from 1996 and the original Itchy cartoon in the episode is from 1919 means that Lampwick would be well over 100 years old.
Judge Snyder’s skin is yellow instead of brown in this episode.