Luigi keeps his diary in a secret basement under his and Mario's house. To find it, go into the bedroom and find a section of boards that are uneven. Perform a Spin Jump on them to open the hidden passage and to read the diary. If you manage to read the entries, you can find one entry reveals that Luigi is afraid of ghosts, and another where he says he wants to have the lead role in his own adventure. These diary entries are referencing Luigi's Mansion (2001), which was in development at the time.
At one point in the game, a whale says "They really should call you Doctor Mario", a reference to another of Mario's classic roles.
The number 64 is prominent in the game. Instances include the name of the train, the name of the bar near the port, and the number of Star Pieces that can be obtained from Chuck Quizmo's quizzes.
This continues the tradition of Mario's adventures ending with a parade of some kind or another featuring all of the characters.
In Boo Mansion, if the player goes through the door across the hall from the entrance and jump in the jar inside, Mario will come out of the jar looking like his original 8-bit sprite.