Bart's catchphrase in this episode is an intentional call back to an episode in the first season of The Simpsons where it was the catchphrase of Krusty the Clown.
During the production of this episode, Late Night with Conan O'Brien had not begun filming and Conan O'Brien had only auditioned for the job, but a scene involving a version of The Conan O'Brien Show was written into the episode anyway. At the point of recording the dialog, O'Brien had got the part as presenter of the talk show, but believed it would have been cancelled by the time that the Simpsons episode would air.
The design of the insides of the box factory featured in this episode was discussed at great lengths by director Susie Dietter and Executive Creative Consultant Brad Bird. Bird wanted the design to be more lively but Dietter wanted it to be more boring to go with the story. Dietter's design was used in the finished episode.
A scene where Bart gets Krusty a danish is similar to the Mean Joe Green Coca-Cola ad. Krusty gives Bart a towel and Mean Joe gave his child admirer a jersey.
Deleted scenes from this episode include Bart sorting Krusty's mail (by either death threats, paternity suits and both) and Homer questioning Krusty on the money Bart is making.
The Simpsons theme had recently been named by the readers of TV Guide as the most annoying theme ever, topping a list of worst theme songs. An intentional reference to the list is made near the start of the show: Bart is whistling the Simpsons theme tune and Marge tells him not to whistle "that annoying tune". Bart also broke the 4th wall.
A dream sequence has Bart playing Match Game 2034 (which includes Farrah Fawcett, despite that she would die in 2009 -- unless 2034 technology will have the ability to bring dead celebrities to life and make them look younger), where Bart sits next to a celebrity's head in a jar. Celebrity heads in jars are prominent in Futurama.
It should be noted that this episode was written before her death.
Krusty alludes to the popular board game Clue when he calls Bart and tells him that he needs his fingerprints on a candlestick and to meet him in the conservatory.
One of Lisa's imagined future achievements, in addition to curing all disease and ending war, is a reunion of the entire cast of long-running sitcom The Facts of Life, "including long-time holdout, Tootie." There was such a reunion as a TV-movie in 2001; Kim Fields returned as Tootie, but Nancy McKeon did not reprise her character of Jo.
Bart records an "I Didn't Do It" rap with the backing track from MC Hammer's "U Can't Touch This". The backwards jeans on the album cover reference the then-popular hip-hop group Kris Kross, who famously wore their clothes backwards.
The chalkboard gag "My homework was not stolen by a one armed man" refers to 1993 film The Fugitive, where the lead role is framed for murder by a one-armed man.
The song young Homer is singing as a one-man band is "Tighten Up", a number one hit in 1968 for Archie Bell & the Drells.
When Lisa complains that Bart's biography was rush-released and "not even about him", this may refer to Vanilla Ice's largely inaccurate, also rush-released biography.