The first episode features a segment in which Yakko, Wakko and Dot sing a song called "Freakazoid and Friends" to the tune of the Animaniacs theme.
"The Freakazoid" has a scene where Wakko randomly shows up after a person calls the titular character a wacko. He tells Freakazoid that he thinks Animaniacs is Steven Spielberg's favorite show. Then, the Brain shows up to argue that his show is better. Then, all three begin a big argument about it. When they address the problem to Steven himself, he wonders who these three characters are.
The Mask: One episode has Stanley meeting his favorite cartoon characters, the Goofalotatots: a skunk, a beaver, and a squirrel who are very obvious spoofs of Yakko, Wakko and Dot — and are actually voiced by Rob Paulsennote Who actually voices Stanley Ipkiss in the cartoon, too!, Jess Harnell and Tress MacNeille.
A sketch from "Kramer Vs. Showgirls" has Michael Moore interview Pinky, who reveals that the Brain's big noggin was the result of Paget's Disease. Pinky also reveals that he has a giant human ear on his back, a reference to the "Vacanti mouse"note a lab mouse who had been seeded by cow cartilage cells, causing the growth of a cartilage structure resembling a human ear.
A sketch from "Eviscerated Post-Coital by a Six-Foot Mantis" features Pinky and The Brain going on a psychedelic trip. Maurice LaMarche reprised his role as The Brain for this sketch.
A sketch from "Cheese Puff Mountain" features Yakko singing the Kama Sutra, parodying the "Yakko's World" and "All the Words in the English Language" sketches from the show.
In the Spring Break Special, the deer in the prologue is from Bumbie's Mom. In the same special, Pinky and the Brain make cameo appearances as two of the caged pets when Elmyra announces that she is going to catch the Easter Bunny, who she believes is Buster Bunny. (The epilogue to the special confirms this to be true.) The Warner siblings make a brief cameo as well, once again doing their literal Running Gag of being chased by Ralph.
In "Night Ghoulery", Fifi is dressed like Dot in the opening credits. In the same special, Baloney and Mr. Director appear in "The Devil and Daniel Webfoot" sketch, where they are in line for the Devil's autograph. The Brain also makes a brief cameo in the "Frankenmyra and Dizzygor" sketch, and the gag credit for the special acknowledges his cameo.