The planet where Wander and Sylvia encounter Dr. Screwball Jones is Cluckon, the chicken-infested planet Hater infiltrated in "The Funk".
The Museum of Ginormous Antiquities from "The Tourist" reappears as the first place Dr. Screwball Jones went to.
The scene where Wander lets Hater go is a reference to the ending of Harry and the Hendersons (1987).
Gelatinous Bob's is a parody of the famous children's restaurant chain, Chuck E. Cheese's.
"The Boy Wander" has various references to Batman. The episode title is a pun on "the boy wonder", which is what Batman calls his sidekick Robin. Dr. Screwball Jones always being manically crazy is similar to the Joker villain. When in hero mode, Wander's voice becomes deeper and more husky, sounding almost like Batman did. The transition scenes are also reminiscent of the original 1966 show.