Honestly, we’ll set pure-CGI aside (though I’d probably vote Gollum in the LotR movies).
For pure animation quality, I’d say Production I.G., for their animation work on both of the following;
Ghost in the Shell: Stand Alone Complex (both seasons)
Near-human (though idealised) proportions, realistic mechanical design, excellent fire, smoke, and other environmental effects. Great use of lighting and cell-shading to suggest realism (even cell-shaded CGI). Across the board this show does a great job of realism for a cartoon, especially for anime, known as it is for emphasising style over realism. But still images don’t do this show justice. The greatest thing about the animation is seeing it in motion, it all moves so smoothly and with such an authentic look it’s amazing.
The storyboard artists also have a great flair for the dramatic, using very striking visuals, in addition to slipping in a lot of subtle details and symbolism. The representation of the various “cloaking abilities” shown, as well as the virtual environments the characters use to browse the internet with are very striking and creative as well.
This show mixed a lot of different looks. Setting aside the entertaining South Park parody, and the manga-style storyboard sequences, this show used a lot of high-end CG special effects and touch-up work to give their work a very visually impressive look, while still maintaining a very sketchy, simple anime looks to the characters. It fit the overall schizophrenic, disjointed feel of the show. The use of various animation techniques and effects to enhance drama, action sequences, and even to add impact to the jokes, parodies, and satirical scenes, is all very cleverly done. Over all the most interesting thing is how well the landscapes and backgrounds are drawn to create a very surreal, dreamlike feel.