Currently, Skull Island's Kong, the Forbidden Journey dementors, and Hondo in the Smuggler's Run pre-show are top contenders. And as simple as they are, I've always loved the subtle movements given to all the presidents in Hall of Presidents. Ursula in Little Mermaid is a pretty underrated one, too.
All-time, Kongfrontation's final Kong, the Xenomorph(s) and the Wicked Witch from The Great Movie Ride, and the "chasing" Carnotaurus from Dinosaur are very high on my list. Also the Pirates Auctioneer... before Disney destroyed the scene.
And, of course, the Expedition Everest Yeti when he worked, which I was lucky enough to experience once before he was turned off.