The scene where Homer hides in a closet and hears that Poochie will be killed off is a reference to Jay Leno supposedly hiding in a closet and hearing that he would replace Johnny Carson on The Tonight Show.
Roy is largely based on Fonzie, calling Homer and Marge Mr. and Mrs. S, similar to how Fonzie refers to Mr. and Mrs. Cunningham.
Roy saying he will move in with "two sexy ladies" is a reference to the sitcom Three's Company.
Krusty exclaiming his disappointment and wanting "chinese cartoons" may refer to programming trends at the time around the mid 1990s, when cable and basic channels began to pick up Japanese anime like Sailor Moon, Pokemon, and Dragon Ball for their immense cost effective profit dividend payoff margins and providing rarely made content and entertainment value outside of slapstick and conventional superhero fare; unsurprisingly, Krusty in this case is also reflective of many opinions of executives who saw little else but the business in this importing boom. The opinions of the kids at the focus group wanting a "down to earth animated show with magical robots" also appear to hint to anime and even sentai/"Power Rangers"-esque series and their rise in interest as well.
On the Krusty cereal box towards the beginning of the episode, Krusty is missing the hair on the top of his head.
On the Krusty cereal box the side Lisa is looking at Krusty is missing one of the side pieces of his hair
For a frame in the final Itchy & Scratchy cartoon of the episode, Scratchy's skeleton is missing its spine.
In Krusty's office the poster with Mr. Teeny his fur is pink instead of the usual brown