Roger Meyers, Sr. being cryogenically frozen is a reference to the myth that Walt Disney's head was similarly frozen.
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.
As pointed out in special features, the film case changes color from black to pink after it is tossed in the garbage.
Judge Snyder's skin color is yellow in this episode. His skin was black for the first nine seasons.
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.