I voted for Jar-Jar, more based on the fact that he was a horrible character. The CGI was also cartoonish, but not really the worst I've ever seen.
As for the I Am Legend zombies, Scooby Do and Garfield...their CGI designs were atrocious. And Ang Lee's Hulk, I thought, looked pretty silly.
But really, there are even worse characters that should have made this list, at least in terms of appearance. The Scorpion King for sure, also the Mummy himself whenever he was all (or mostly) CGI.
Most of the new Transformers in Revenge of the Fallen looked like crap. They didn't necessarily look fake... but most of them were a complicated mess (especially Devestator) and it was often difficult to tell what the hell you were looking at. And ALL of their personalities sucked.
The designs weren't terrible, but I'd have to say that all of the characters in Final Fantasy: The Spirits Within sucked. Every single one had the personality of a toaster oven.
The alien and the Dr. Smith monster in Lost in Space were awful. Actually, everything in that movie was awful.