Some of the photoshopped images of Krusty feature him as: Neil Armstrong, the soldiers at Iwo Jima, the Tank Man, and Jim Leavelle, the Texas homicide detective who was escorting Lee Harvey Oswald when Oswald was shot and killed.
Mayor Quimby's quip about his regretting building his lover an opera house after hearing her voice for the first time was a reference to Citizen Kane in Rosebud, specifically his making a similar mistake.
In Krusty's campaign commercial, the voiceover saying "The man from funny" is a parody of an ad for Bill Clinton in 1992, where Clinton was a the man "From a town called Hope"
When the plane hit the living room of the Simpsons' house, it reversed by itself. A plane cannot reverse by itself, it will need a pushback car or must turn around.
When Krusty says he's on Pepto and Xanex, Marge's pearls and Lisa's dress turn to a light orange.
Planes can't fly so low.
Marge says the family haven't had a decent night's sleep in weeks, however flights aren't allowed to operate between certain times (night).
Krusty's navel can be seen when wearing the tank-top in his offensive sketch.