I'm with Aerith on this one... Maleficent was one evil bitch... I mean, you can't get much more evil than opening youself up to the powers of Hell and taking on the form of a demonic dragon. That shit was freaky as a kid and totally badass now. She was, and always will be, the ultimate antagonist from a kids film.
http://youtube.com/watch?v=6ukymvPDzaQ
A distant second would be Galvatron (the reborn form of Megatron after his run in with Unicron in Transformers: The Movie), if only becasue of his totally badass nature, and the things he did that Megatron should've done years before. It was like he was Megatron on steroids and had forgotten to take his chill pill... not to mention he looked cooler, and his transformation was a canon rather than a pistol... granted, he was Unicron's bitch, but thats beside the point... he was still badass.
http://youtube.com/watch?v=yLtzA0A7w90
There are others that come close to Galvatron... but no one can touch Maleficent, imo... she
is the most evil antagonist in a kid's movie... plain and simple.