"Superman: Doomsday" is the first animated Superman project to be rated PG-13.
Kevin Smith appears animated as himself with one line: "Pff, like we really needed him to bust up the mechanical spider right? Lame!" This is a reference to the requirement made by producer 'Jon Peters, that Kevin Smith include a giant spider in the film 'Superman Lives', to be given the position of director (the project was canceled, in favor of Superman Returns (2006)). Kevin Smith wanted to use the same basic plot of 'Superman: Doomsday' for 'Superman Lives'.
Superman's black suit, and longer hair when he came back to fight the Doppleganger Superman is one of the few things to match up with the comics.
In the scene where Luthor and Mercy are discussing his cure for muscular dystrophy, he mentions having "Swan" and "Shaffenburger" work on it. Curt Swan and Kurt Schaffenberger were two artists who drew Superman for DC Comics in the 1970's.
In the Fortress of Solitude various items can be seen from past Superman cartoons. Some of these include Superman's Space Suit and Rocket from Superman: The Animated Series (1996). Others are from the Fleischer Superman cartoons of the '40s including the Bullet Car from Superman: The Bulleteers (1942) and one of the Robots from Superman: The Mechanical Monsters (1941). The Bottled City of Kandor can be seen as well.