Beatallica, being partially based on the band Dave Mustaine was kicked out of, has a few references to him, particularly the song "Mean Mr. Mustaine" (whose melody combines The Beatles' "Mean Mr. Mustard" and Metallica's "The Four Horseman", whose melody Megadeth repurposed into "Mechanix").
Duck Dodgers: The episode "In Space, No One Can See You Rock" has Dave being revived to use The Power of Rock against Martian Easy Listening, culminating in the full line-up Megadeth performing "Back in the Day".
In "Sideshow Bob's Last Gleaming", some soldiers try searching for Sideshow Bob in Hangar 18.
In "Million Dollar Abie", Grampa goes to a doctor that practices assisted suicide and gets hooked up to a euthanasia machine that looks like a giant iPod. One of its modes of death is "Megadeath".
In "Springfield Splendor", Lisa goes to the school's psychologist about a recurring dream, and she looks into a book listing dreams and what they could mean. It says that dreams about Megadeth mean "Sex", those about "Megasex" mean "Deth".
