Toy Story set the stage for future animated films, and all animation in general. The makers took a hit or miss chance, which turned out to be the biggest hit in the world of computer animation. If anyone has not seen "the pixar story" I highly recommend it.
But for personal favorites I say it's between "WALL-E" and "Over the Hedge". Nothing beats the squirrel drinking coffee in Over the Hedge.
Wall-e has such a chilling message behind it, it's chalked up with my overall favorites. I'd have to say Over the Hedge is quite a genius concept. I also really liked the Gundam Wing Zero movie back in the day and Endless Watz.
and list of top animations
Kung Fu Panda
Wallace & Gromit
Cloudy with a Chance of Meatballs
The Little Mermaid