Zach doesn't want to go to his Dad's alma mater, Dartmouth. His dad is played by Tim Matheson who starred in Animal House (1978), which was partly inspired by the time of of the film's writers spent at Dartmouth. At the end of "Animal House", Matheson is said to move to California and become a doctor . . . which he is in this film.
The character "Brock Hudson" was actually named after a real-life student of the same name at St. John's School in Houston, Texas, the same school where Rushmore (1998) was filmed. Screenwriter R. Lee Fleming Jr. went to this school, along with Wes Anderson (director of "Rushmore") and Will Wallace, where the phrase "what kind of name is Brock Hudson?" (used twice in this movie) was commonly heard.
The film contains several hidden references to the pop group Hanson, aside from the photograph during Taylor's campaign. The two main characters are named Taylor and Zac - two of the members of Hanson. Mackenzie, and Jesse - two minor characters, were younger members of the Hanson family.
Freddie Prinze Jr. and Matthew Lillard appeared together again in the Scooby-Doo movies, as Fred and Shaggy. Those movies also featured Sarah Michelle Gellar (mentioned in another trivia item here) as Daphne.