The anime cartoon that Bart watches is a parody of Pokémon. Additionally this episode also aired on the same day that Pokémon HeartGold and SoulSilver, the remakes for the Pokémon Gameboy Color games Gold and Silver were released on the Nintendo DS in the United States.
The filmstrip at the beginning contains some classic cartoon sound effects, such as the "pbpbpbpbpbpbpbpb' motors from The Jetsons and the trombone talking of the teachers in the Peanuts specials.
The music being played in the film strip and during the credits is George Gershwin's "An American in Paris".
Bart and Milhouse both make Thomas The Tank Engine references when they discover the subway.
Mrs. Krabappel says that Bart ruined every ideal she had about teaching since she saw the movie To Sir, with Love as a little girl. This leads to Nelson telling her she's 'old', which is a reference to Mrs. Krabappel's voice actress Marcia Wallace being 67 at the time the episode first aired.
Moe's Express is a parody of Panda Express.
According to a painting in the subway station, the Springfield sign was built as "Springfieldland", just like the original Hollywood sign was build as "Hollywoodland"
About 8 minutes into the episode, Lisa's pearls briefly appear red like Marge's, a goof commonly seen in episodes.
When Lisa was explaining her example fraction equation's answer, it is incorrect. 1/2 + 1/3 does not equal 3/anything. It equals 5/6 minimum. However, she could've meant 3/6 + 2/6 instead.
Despite the subway system being abandoned, it is still used in various couch gags.
It is unknown how Springfield Elementary got rebuilt after the bulding has been destroyed.