He's been on South Park quite a few times. There was an episode from Season 8 (2004) that largely defended him against the allegations actually, Season 13 (2009) and last year as a hologram (Season 18). I remember his name was also dropped in a Season 2 episode (1998) as well.
Not really a surprise since South Park parodies everything and anything, but still pretty cool. I remember there was a Simpsons episode where Bart and Milhouse break into Ned Flander's house and they find a room completely decked out with Beatles merchandise. Homer comes in later and goes over to some bobbleheads of the fab four, puts on falsetto voice and goes "Now I'm Michael Jackson! I own all your songs! Hee-hee-hee!".
When it comes to movies, I also remember watching Back to the Future II a few months back and there's crammed with MJ references, I remember Marty McFly broke into his house in an alternative timeline, only to find out it was someone else's house. Anyway, the room he broke into was a kid's room and full of Michael Jackson Thriller posters etc. Of course there's that 80s bar that plays Beat It and has some weird MJ like animation on the TV screens. The Rush Hour series (especially #2 I think) has many MJ references too.
That's a few off the top of my head.