I have to agree with a lot of the people here: in terms of pure CGI, as opposed to composite model work, Avatar takes the cake.
Some shots work better than others, no question, but when Avatar is at its best, there really isn't any comparison. When I looked into how a lot of this the forest stuff was put together, I expected some degree of composite work. But there isn't any. That's pretty incredible, frankly. Several shots just look and feel completely real to me. The reveal shots of Neytiri are closer to photo-realistic than anything I've ever seen.
Runner up, of course, has to go to the T-Rex scene in Jurassic Park. While some of the CGI in that film has not aged well at all, ILM created work in that one scene that will last forever.
Honorrable mention to Children Of Men, because it always gets forgotten.
It's mostly composite work, especially the long-take scenes, but its utterly convincing to me. Some bad CGI in there, of course, but when its good, its damn good.