The scene where Chris was arguing with these people in a restaurant and his mother yells at him. In response, he yells back, and as a result, the music from Kill Bill plays, and the next scene involves Chris in the hospital with his mother's shoe lodged in his rear end.
"You can take your breakfast, and eat it in HELL!"
For that matter, the entire scene where Eustace is arguing with the hunched back stranger.
The disembodied head from "The House of Discontent" being replaced by the Mario head from Mario Teaches Typing 2: "Begin typing now, or suffer!" And just when it's about to kill Eustace for his impertinence:
Muriel: Please have mercy on us. (King Harkinian pops up) Mario:DON'T SAY IT! (King Harkinian goes away, Mario continues charging his beam)
Recreating one YTP intro theme using SpongeBob, Squidward, Mr. Krabs and Patrick's peeking noises.
The dreaded "V of Doom" appearing when Squidward declares he has no soul.
Squidward: Put my windows back!
SpongeBob: Sure, Squidward.
(SpongeBob and Patrick put their reef blowers in reverse and shoot the pieces of Squidward's house back at it. The pieces freeze in midair, the camera keeps switching between them and the pieces during which a random anime woman appears, then the pieces fly back at them blowing up Bikini Bottom)
In Rolf Rapes Reality, Edd, of all people, kills Justin Bieber by belching. This immediately leads to a Caramelldansen dance party.
In the Christmas episode "Skellington's Revenge", all of the characters are giving their Christmas wishes to SpongeBob. When he gets to Chris, he asks him what he wants Santa to give him. Chris responds by asking Santa for a Playboy Magazine, to which SpongeBob tells him that he'll shoot his eye out. The scene then cuts to Chris being stuffed into a bottle.
In the same special, SpongeBob explains to his friend Patrick that he invented a device that could be used to shoot the President. Cue the text explaining the scene away as a joke.
Jack, who's high on cocaine, throws a sheep with his head on it at the Mayor when the Mayor won't leave him alone.
"I CAN FLY!"
SpongeBob asking Jack (who's disguised as Santa Claus) where his big, round belly is. Jack responds by grabbing him and saying: You naughty little shit! HOW DARE YOU CALL ME FAT?! SpongeBob apologizes out of fear, and Jack throws him down.