Close Encounters of the Third Kind - Homer obsessively sculpts a circus tent out of mashed potatoes at the dinner table. Roy Neary does the same thing with the Devils Tower, sculpting it in various media throughout the film, starting with mashed potatoes at the dinner table.
Krusty bets on the Washington Generals who regularly play the Harlem Globetrotters. Currently (11/2011) the Globetrotters have a 98.4 winning percentage. (Again citing Krusty's awful gambling skill)
Starsky and Hutch - At the Cable ACE awards, a voice-over announces that the son of the actor who played Huggy Bear will accept an award. In actuality, Antonio Fargas played Huggy Bear and his son is Justin Fargas, a running back for the Oakland Raiders, who does not dress like Huggy Bear did.
When the mob runs out of bullets after creating speed holes at the car dealership, Fat Tony says "Let's go to Big 5." Big 5 is a sporting goods store which sells bullets (for hunting).
On the audio commentary, Matt Groening believes that this was also used for an O.J. Simpson reference (OJ possibly bought a knife at Big 5, according to Groening)
When Homer and Krusty are riding the tricycle for the mob, Homer hits his head on several hanging wine glasses. The pinging sounds like the love song in The Godfather, heard when Michael Corleone is hiding out in his ancestral homeland of Italy and gets married to his first wife.
One of the objects Krusty burned to light up his cigarette was a copy of Action Comics No. 1, one of the, if not the most expensive comic book ever.
Krusty throwing the mirror to the floor after seeing the results of his plastic surgery refers to Jack Napier's similar action in Batman. It also mimics Lisa's reaction to her braces in 'Last Exit To Springfield'.
Krusty shouting at phone "Well Excuuuuse Me!" was referenced to cartoon tv show based on Nintendo video game Legends of Zelda when Link repeatedly shout same thing at Princess Zelda.
Krusty has his accountant send three thousand roses to Bea Arthur's grave, even though she was still alive at the time (as his accountant tried to point out). However, Bea Arthur did eventually pass away in 2009.
In the episode 'Homer Goes to College', Bart asked, when learning that Mr. Burns wanted Homer to go to College, if he meant Barber College or Clown College.
We learn Homer's favorite parts of the first of the month are new billboard adverts.
Krusty used $48 to franchise his name.
Krusty burns his cigarettes with 100 dollar bill, an Action Comics No. 1, and a Pearl Necklace.
Pearls are not flammable. They could be faux pearls.
When Homer arrives at the Van Houten house for Milhouse's party, Janey is among those at the entrance and she appears with yellow skin than brown.
When Krusty uses a $50 bill to retire his debt of $48 to the Mafia, the Mafia Don returns $2 to Krusty but uses three bills to do so, despite $1 being the smallest denomination of American money in bill form.
Krusty's breast implants conveniently have disappeared when he returns to America. It seems unlikely he could have had them removed due to his lack of funds at the time.