Eat My Shorts is a horse running in another race (and another of Bart's catchphrases).
There is a large drum of nuclear waste seen in Homer's basement in this episode.
Bart's forgotten permission slip can be seen (just barely) under his pillowcase before he wakes up at the beginning of the episode.
While imprisoned, Bart's cellmate is a seriously pumped-up Sideshow Bob. Sideshow Bob does not speak in this episode, presumably because he may be contemplating how Bart, who got him arrested in Krusty Gets Busted, is now an accused lawbreaker himself.
During the last scene the Simpsons watch a movie based on this episode. When the narrator lists the actors, the actor playing Fat Tony is Joe Mantegna, who provides the voice of Fat Tony on The Simpsons.
The producers attempted to have "Be My Baby" by the Ronettes play midway through the episode. Due to being unable to secure permission, they used "One Fine Day" by the Chiffons instead. Be My Baby was famously used in Mean Streets, Martin Scorsese's breakthrough film.
On the news, Fat Tony's real name is revealed as "William "Fat Tony" Williams" but would later change to "Anthony "Fat Tony" D'Amico" in "The Homer They Fall," though the different names could be aliases, as Fat Tony is a mob boss and would need fake names to keep law enforcement off his tracks.
The Indian shown in the film on the field trip is akin to Chief Yahoo, who allowed his caricature to be used as the mascot for the Cleveland Indians.
In this episode Seymour Skinner is shown as having his own house, but later in the series he is shown as living with his mother. He could've later moved in with her, or vice versa.
One of the rumors of Skinner's assumed murder is that the cafeteria made his corpse into hamburgers. In "Treehouse of Horror V", many Springfield Elementary students would be turned to food to solve the school's problems with overcrowding and budget cuts to the lunch program.
The footage of Smithers showing Mr. Burns the newspaper headline about Bart is recycled from Brush with Greatness.
This episode takes a lot of plot points from the film Goodfellas. As in the film, a boy mixes drinks for the mob gang, and there is also a cigarette hijacking. Bart's work for Fat Tony mirrors the rise of young Henry Hill.
Psychic Princess Opal's line, "I'm afraid it's splitsville for Delta Burke and Major Dad" is a reference to then-tabloid fodder Delta Burke and her husband Gerald McRaney. Ironically, Delta Burke and Gerald McRaney are still together as of 2016 (they married in 1989).
In the scene in which Edna Krabappel is grieving over Seymour Skinner's absence, among the students who are there, Becky, is seen wearing green instead of the usual turquoise. She could've chosen to wear green that day.