I'm not familiar with the show myself, but according to this story from Toon Zone, composer Michael McCuistion used a theremin in the score to the cartoon Teen Titans episode, "Every Dog Has His Day" (Warner Bros). In the episode, aliens appear and mistakenly abduct the wrong dog (who is apparently some kind of super dog).
I'm enjoying this trend of theremin music showing up in more and more mainstream media, even if it's still primarily adding mood for aliens and flying saucers.
The episode will be featured on the DVD, "Teen Titans: Fear Itself" to be release Sept. 20th, 2005.