For 3D games, probably Soul Calibur. Not only was it probably the best-looking early Gen 6 title, but Gen 5 3D titles in general looked terrible so they all get disqualified by default (though the ones like Super Mario 64 that went for really cartoon-y aesthetics fared better).
For 2D games, I want to say Street Fighter III. Those sprite animations were so detailed and fluid:
In fact, SF3 makes me wish more developers would have kept making 2D sprite-based games into Gen 5 and beyond. Instead, 2D was largely abandoned in favor of 3D, with a few companies like Capcom making the occasional 2D game.