- Bizarro Episode: "How I Spent My Weekend" is told from Elmyra's perspective and animated through her drawings on lined paper. Bizarro just doesn't begin to describe how weird the episode is.
- Creator's Pet: Elmyra, who is basically the reason the show was created.
- Critical Dissonance: In contrast to the hatred the fans have toward the show, it actually got critical acclaim and won various awards, including an Emmy.
- Ensemble Dark Horse: For all the problems with this show, its antagonist Wally Faust left quite an impression in some viewers' eyes. He does look and talk like an evil Christopher Walken, after all.
- Fanon Discontinuity: Brain isn't the only one who deeply resents this show.
- "Funny Aneurysm" Moment: "A Walk in the Park" has a Running Gag where Brain gets trampled by an oncoming parade at a Disneyland knock-off. Five years after the episode aired, a cast member dressed as Pluto died when he was run over by a parade float in the Magic Kingdom.
- Ho Yay: Occurs in "Pinky's Dream House," where Pinky acts like a housewife to Brain and even sings a song about how happy they'll be together before Elmyra makes his dream come true.
- Also Elmyra and Vanity White, one-sided on Elmyra's part (Vanity, like most people, can hardly stand her.)
- Misblamed: For years many viewers believed Kids' WB! executive Jamie Kellner to be at fault for the creation of this series. However, during one episode of Talkin' Toons' with Peter Hastings, it was revealed that the network, despite what the theme song says, did not meddle with the series — it was, in fact, entirely Steven Spielberg's idea!
- Narm Charm: In "Pinky's Dream House," Pinky sings a deliberately cheesy and cutesy song about how happy he would be if he and Brain lived in a tiny house together. Like most of Pinky's flights of fancy, it's not meant to be taken seriously; but for some viewers, it's just so darn cute and sincere that you can't help but crack a little smile.
- Never Live It Down: A big one for Warner Brothers, having caused the cancellation of Pinky and the Brain to promote a considerably less popular cast member. On top of that, it's well known to most that nobody involved in its production wanted any part of it.
- Replacement Scrappy: Rudy Mookich for Montana Max. Elmyra's most frequently seen pets were now Mr. Pussy-Wussy and Mr. Shellbutt, taking the places of Furrball and Byron Basset (in "The Ravin!", we see that Elmyra has a pet cemetery - maybe she squeezed them to death?).
- The Scrappy: While Elmyra was already plenty unpopular for getting way too much attention over the more beloved characters from her original show, this one pretty much finished the job that Tiny Toons started by forcing other more-beloved characters (one of whom was already "the dumb one") to share screen time with her and ensuring she'd go down in history as one of the most loathed cartoons characters ever.
- Signature Line: The line from the opening theme, "It's what the network wants, why bother to complain?", aptly summarizes the feelings both the writers and fans had for this spinoff.
- So Okay, It's Average: A minority of viewers have said that, while the setup and characters were doomed from the start, this is still written by the same writers who had created all of the best episodes of Pinky and the Brain and, therefore, had plenty of clever gags and stories sandwiched between everything else that brought the show down. It helps that the show does in fact self deprecate its own ridiculous premise routinely, even if it does little to prevent it still occurring.
- Take That, Scrappy!: One of the show's biggest redeeming factors is that it spends half the time being self aware and mocking what a third wheel Elmyra is.
- Tear Jerker: Brain's line near the end of the opening, "I deeply resent this" can come across as one. Not only does it echo Maurice LaMarche's feelings about the Retool, it's almost as if he knew it was going to flop.
- They Wasted a Perfectly Good Character: The show might have stood a chance if Wally Faust appeared more frequently. He can be quite the Manipulative Bastard, after all.
- They Wasted a Perfectly Good Plot:
- The series would have been a lot better with the rest of the Tiny Toons cast instead of the replacements mentioned above.
- The basic setup of Pinky and the Brain becoming pets to a naive little girl could make a pretty decent cartoon, if only the new series idea had been arrived at organically with a crew that actually wanted to do it. In fact, the show staff had earlier paired Brain up with Mindy from the Mindy and Buttons segment in an episode of Animaniacs. And the result is arguably much funnier than what this series put out.
- Took the Bad Film Seriously: Rob Paulsen won an Emmy for his performance as Pinky in this series. In fact, the whole series can be described as this in probably the most confusing way — there's a clear number of Biting-the-Hand Humor and Take That! moments aimed at expressing the whole resentment the staff had towards this concept, but in spite of that, the show still has the same quality of animation as the original cartoon and the acting is still just as good as it ever was, even if the writing wasn't always up to snuff. For those reasons, the show does get its defenders, and even The Nostalgia Critic admitted that the show could be Actually Pretty Funny in spite of how much the concept was doomed to fail from the start.
YMMV / Pinky, Elmyra & the Brain