As long as we're including movies, because that's where most of my knowledge for 3D anime comes from, I'd say .hack://Beyond The World. It doesn't really stand up animation wise all that well now, in fact it kind of looks like Code Lyoko in terms of animation, but I like it. It has a good story, the characters are really believable, and it did a good job convincing me at the time that anime being in 3D might not be all that bad. Too bad it turned out that movement had to become more plastic looking as time moved on, or that it got mixed with far superior 2D animation, but for the time, I had hope of the idea succeeding.