- Creator Backlash: During the show's own theme song, no less! It's understandable however as the staff and cast did not approve of this change in direction from the outset.
- Creator Killer: The series, plus the rising popularity of Pokémon on Kids WB, ended Steven Spielberg and Tom Rugger's partnership which had began with Tiny Toon Adventures. Rugger and many of his collaborators for these shows, such as Sherri Stoner and Paul Rugg, struggled to find work for a few years after.
- Executive Meddling: This trope gained a combined Take That! and Lampshade Hanging in the form of the retool-explaining Expository Theme Tune: So Pinky and the Brain / Share a new domain / It's what the network wants / Why bother to complain? At the end of the song, Brain laments "I deeply resent this."
- Franchise Killer: Before the Retool, Pinky and the Brain was a mega hit shown on prime time. Five episodes later, it was cancelled. It also wound up being the last collaborative work between Warner Bros. Animation and Amblin Entertainment as a result.
- Keep Circulating the Tapes: This was the fate of the show for the longest time before finally getting a complete DVD release in 2014. Due to the show's reputation, many would be fine if it were to stay unreleased.
- Old Shame: Nearly everyone who worked on this thing (Maurice LaMarche (The Brain), Rob Paulsen (Pinky), the writers) hated it with a passion. So much so that the theme song takes pot shots at the idea.
- Technology Marches On: One episode has Brain planning to switch the background music of an amusement park ride with a subliminal message he recorded using audio cassettes as the medium. At the time the series aired, tapes were experiencing their last breath of relevance as compact disk (briefly) was becoming the most popular music format.
- Too Soon: "A Walk in the Park" has a parody of Shari Lewis and Lamp Chop (called Marie Flewis and Pork Chop) that was somehow left intact considering Lewis passed away of uterine cancer six months before the episode aired.
- Unintentional Period Piece: The show made references to several late 90's bands and TV shows, including Bill Nye the Science Guy, Teletubbies, and Hanson.
- Word of God: Officially confirmed to be non-canon
- Writer Revolt: The writers were extremely dissatisfied with the Executive Meddling they had to endure. Peter Hastings not only wrote the episode "You'll Never Eat Food Pellets in This Town Again", but later left Warner Bros. altogether to create Disney's One Saturday Morning.
Trivia / Pinky, Elmyra & the Brain