Doctor Johnny Fever makes two quick references to Shakespeare in a Season 4 episode. The plot surrounding the allusions isn't important, so I'll ignore that.
The first reference contains an allusion to Dick the Butcher's famous line from 1 Henry VI: "The first thing we do, let's kill all the lawyers" (IV.ii.76-77). Well, it's a very rough paraphrase, but Johnny Fever does cite Shakespeare as the source.
The second is just the name "Othello" uttered after Dr. Fever takes a closer look at what Venus Flytrap is wearing.
Links: The Episode at IMDB.