According to the DVD commentary, the scene where The Spleen (Paul Reubens) accidentally ignites a blast of flatulence standing by a barrel with a fire in it was a happy accident. Apparently, a crew member had tossed a plastic lighter in the barrel. It happened to explode (a small explosion, but an explosion none the less) while filming Reubens. The reactions that followed were created after the fact, capitalizing on the moment caught on film.
A subtle reference to William Shatner: once, while recording lines for the Interplay Star Trek video game Judgement Rites, Shatner pronounced "sabotage" strangely and was asked twice to repeat the line. He finally blurted, "Don't tell me how to act - it sickens me!" In Mystery Men (1999), this line is repeated by Ben Stiller. Later, Janeane Garofalo says to Stiller, "You say 'sabotage', I say 'saboTAGE'," another Shatner quote from the Star Trek recording session.
The Mystery Men were the supporting cast of an underground superhero comic book called the Flaming Carrot. Mr. Furious and the Shoveler were the only ones from the comic to make it into the movie. Captain Amazing was created as a replacement for the Flaming Carrot, who was felt to be too bizarre to bring to the silver screen.
As the team enters Dr. Heller's amusement park workshop, creepy music is heard. This is not just incidental music, but turns out to be Dr. Heller practicing on a 'waterphone', the strange cylindrical device with steel wires he can briefly be seen holding. The waterphone is primarily used in the motion picture industry in the composition of creepy incidental music.
Artie Lange, who has joked about the poor reception of films he's acted in, considers this to be the worst movie he has made. After seeing his brief scene in the beginning of the film, his mother and sister called him from the theater to ask if he would have any more scenes because they wanted to leave.
The two Wonder Women who fight have black and red hair, eerily paralleling the storyline in the Wonder Woman comics where the black-haired Princess Diana is forced to give up the title (and costume) of Wonder Woman to the red-haired Amazon Artemis.
Casanova Frankenstein's castle is heavily influenced by the works of Catalan architect Antonio Gaudi, down to details such as railings, capitals on columns, and the alcove in which Spleen and Invisible Boy cower.
The Bowler's stream-of-consciousness monologue in support of independent filmmaking at the conclusion of the film was originally not intended to be included in the finished print. Janeane Garofalo was instructed by director Kinka Usher to say whatever came to her mind at the time (Usher simply wanted to use up some excess film.) Usher liked her performance so much he edited it into the final print.
The Blue Raja's car is a Messerschmit KR200 Kabinenroller, a three-wheeled bubble car designed by the aircraft engineer Fritz Fend and produced in the factory of the German aircraft manufacturer Messerschmitt in the 1950s and early 1960s.
The Sphinx was a Golden Age hero who was the creation of Better Publishing; his real name was Ellsworth Forrester, and he first appeared in Exciting Comics #2. Had Better Publishing still been in existence at the time this movie came out, the filmmakers could have been sued for plagiarism. As it is, due to the fact that Better went out of business in the 1950s with no successor, the character is now in the public domain.
In an odd parallel, Tom Waits actually creates curious machines from junk and hardware store purchases, in the same way that his character (Dr. Heller) does. Waits' machines are musical, and one is 6-stringed steel dumpster.
There is a subtle reference to the old slapstick gag of the watermelon-and-the-hammer - it's when Mr. Furious, during the Sphinx' strange training session, is wearing watermelon on his feet and proceeds to bash them (off screen) with the tack hammer he is supposed to balance on his head.