From Wikiedia's entry on Mystery Men I learned the film twice references an "infamous audio clip" of William Shatner from a Star Trek looping session (when actors dub dialogue).
1) When evil Casanova Frankenstein [Geoffrey Rush] corrects good-guy Mr. Furious [Ben Stiller], he responds with a direct quote from Shatner.
Here's the exchange:
Mr. Furious: Do yourself a favor and don't punch my clock, 'cause I'm a Pantera's box you do not wanna open.
Casanova Frankenstein: It is 'Pandora'.
Mr. Furious: Uh, please don't correct me. It sickens me. [That's our Bill!]
2) The Bowler [Janeane Garofalo] states, "I say sabotage, sabotage" (pronouncing both A's as in "apple"). Yup. Bill being Bill.
Wikipedia doesn't say, but can we thank Trekkie Ben Stiller for these Shatnerisms? [Ben, above right, giving homage (?) to Bill, 2004, from jamd]