- Creator Backlash: Matt Wilson began liking the show. Then he got some really irritating and stupid fans. Then, he really hated the show and its fans. That he got threatened both if he stopped or continued making the show, and that there were reports of fans stalking him... causing him to justify the hate. Allegedly, he not only renounces Bonus Stage, but he stopped playing video games altogether.
- The Other Darrin: From the second part of episode 75, "The Day the World Did Stuff", on, Elly and June were voiced by women instead of a pitch-shifted Matt Wilson. In Elly's case, it was lampshaded as her apparently having a frog in her throat the whole time.
- Uncancelled: Came very close. After Matt Wilson announced that he was ending Bonus Stage a season early due to financial troubles, a fan offered to pay him $15,000 to continue the series. Nothing ever came of it. It's possible that the entire thing was a cruel prank.
- What Could Have Been:
- Season 8, obviously.
- The plots to seasons 7 and 8 were changed around after season 6 ended. Perhaps anticipating that the series might not make it to an 8th season, Matt wrapped up several of the characters story arcs in season 7. He then left an option open for a more bare-boned (and therefore cheaper to make) season 8, with the 100th and final episode "Thank You for Playing" (in which every villain Joel and Phil had to face over the course of the series return to fight them, forcing the two to recruit all of their allies to counter the villains) being replaced by the much less ambitious "Trial Expires After 30 Minutes" (in which Joel and Phil confront the cloaked villain who killed Rya).
- The Wiki Rule: While no longer up, the Bonus Stage Wiki would detail each episode in great detail, pointing out each and every reference fans could find, and host full scripts of each episode. The show makes several references to the wiki in its later seasons, in one case pointing out the references listed were often incorrect.
Trivia / Bonus Stage