After wondering just how many Pinky and the Brain episodes were made for Animaniacs, I decided to look at the episode listings and do a full breakdown of how many sketches there were for each character/s. For simplicity's sake, I did not include bridging segments and vignettes (Good Idea Bad Idea, Randy Beaman, Dot's Poetry Corner, Wheel of Morality, etc.) except for very consistent ones that are mentioned on the DVD boxes, like Testimonials and Animator's Alley. They went under Warners.
Crossovers are segments where characters from different sketches interact in the same segment for a lengthy time beyond a typical cameo--i.e. the Warner Bros. and Slappy in "Baghdad Cafe," the Warners and Pinky/Brain in "Hercules Unwound," and the whole cast in "Animaniacs Suite." Things like Pinky and the Brain appearing at the end of "A Hard Day's Warner" or Slappy as the tree in "Jokahontas" don't count. The last one is "Other," which are one-shots like "A Gift of Gold," "Wings Take Heart," and "Skullhead Boneyhands." (BTW I counted "Little Old Slappy from Pasadena" as a Slappy sketch and not a song because 1) it uses the actual song and 2) nobody in the short sings it.)
Allow for a small margin of error, especially for the Warners.
Warners: 102
Pinky and the Brain: 18 (plus 65 in their own TV show, one of which was the crossover "Star Warners")
Slappy: 28
Goodfeathers: 14
Rita and Runt: 12
Buttons and Mindy: 14
Chicken Boo: 12
Minerva Mink: 2
Hip Hippos: 5
Katie Ka-boom: 6
Songs: 42
Crossovers: 15
Other: 10
