I don't know if "He-Man" was based on a comic--I think the comic may have been subsequent. "G.I.Joe" and "Transformers" certainly are both worth mentioning. I also have some of the "Thundercats" comics, but I think the comics were probably based on the show.
I also love "Spidey and his Amazing Friends", "Spidey Unlimited", "X-men" (90's), "Justice League" and "JLU", "Teen Titans", "TMNT" (I appreciate the animation of the new one, but thought the first was funnier), "Super Friends" and another previously unmentioned "The Tick".