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.
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