In 22 Short Films About Springfield the scene where Chief Wiggum, Lou and Eddie discuss hamburgers from Krusty Burger and compared them with McDonalds their dialogue is a parody of the famous hamburger dialogue from "Pulp Fiction". The restaurant where they eat their meal is similar to that from "Pulp Fiction". The scene where Snake Jailbird encounters Chief Wiggum while driving and then chases him until they are both tied up by a weapon salesman (Herman) are taken directly from this movie.
In Take My Wife, Sleaze the 1950s restaurant is similar to the one in "Pulp Fiction", including the dance contest.
In A Tale of Two Springfields Homer complains that he already has enough things to remember and a close-up of his hand shows the writing "Lenny=White, Carl=Black." This is a reference to the second last scene in Pulp Fiction, in which The Wolf is called to help resolve a problem. On a pad of paper before he meets up with Vincent and Jules, he writes "Vincent-White, Jules-Black" in order to distinguish between the two.
Homer makes a finger gesture while dancing with the Eskimo lady in The Simpsons Movie that is a direct reference to the dance scene from "Pulp Fiction".
Wikipedia Article for Pulp Fiction