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Although Joker himself never appears in Krusty Gets Busted, he is given an indirect reference by Timothy Lovejoy, Jr., where he refers to Krusty during his sermon as the "Clown Prince of Corruption", a play on Joker's nickname of the "Clown Prince of Crime".
Smithers pays Carl to dress up as the Joker so Mr. Burns can go after him as Fruit Bat Man in "Dark Knight Court".
In "A Test Before Trying", when the school is shut down for bad grades Princible Skinner says to Nelson that he will be atending a school parody of Arkham Asylum, of which The Joker, or at least a man resembling him, appears to be driving the bus, until it explodes.