Of the ones I've played, I would say either Dragon Quest VIII or Wind Waker. But for completely different reasons.
Wind Waker had very technical things behind its graphical improvements. Things like lighting effects, the cel shaded fire/smoke and frankly the stronger textures on the GameCube.
Dragon Quest VIII however had specific other areas where it shined through such as FAR more detail in art design and individual textures. Along with extreme fluid and near seemless integration of all the cel shading, a feat even Wind Waker had problems with at times where some textures would appear blocky or pixelated. As well as probably being one of, if not the biggest cel shaded games in terms of content and scope still to date.
The reason I would probably give the crown to Dragon Quest VIII is simply because from start to finish, the entire package not only is 98% full Cel Shaded, but done so seamlessly, you don't even recognize it. You really do feel like you are playing in the middle of an animated game, and that's what Cel Shading, at least in that style, is all about. Not to mention it was a cel shaded game that pushed some of the major limits for the PS2, and never once folded.
In short, and I hope people don't burn me alive for this analogy, but where Ocarina of Time made that 'big grand step' for 3D gaming in 1998, I feel Dragon Quest VIII did the same thing for Cel Shaded games. It had that same powerful effect for me. In other words, I actually feel the games overall style and cel shading aided the game and was not just a nice athstetic choice.