I think the reason that CGI worked so well in JP & JP2LW was because the computer "puppets" were controlled by match-move stop-frame armatured controlled by traditional animators. Also, the CGI images are so well 'grounded' in the film as well - they're very convincing, especially in JP2.
Agree with peformingmonk about the USS Indianapolis scene from Jaws, and with noops re. the Bladerunner scene.
Another favourite sequence of mine, again from Mulholland Drive (watched it again last night) - the "discrete assassination" scene where the hitman shoots the guy for the "history of the world in phone numbers" book, then while setting up the gun in the dead man's hand to make it look like suicide accidentally shoots through the wall and injures the woman next door, has to then shoot her, but is witnessed by the night cleaner, so he has to then shoot him, who then accidentally switches on his vacuum cleaner while he's falling, so the hitman shoots the vacuum cleaner, causing an electrical short which sets off the intruder alarm. It's such a surreal sequence of events. There are so many wonderful sequences in that film!