It's almost impossible to know what the most realistic CG effects in a movie are as the very best most realistic effects are often invisible.
Obviously it's different if the effects are done to make a dinosaur or something, then that would be different as you'd know that they'd have to use SFX.
Often the best SFX are only apparent when you see a 'making of' TV show which shows how a special effect was put together.
You think "Wow, I didn't even know that was a special effect, I thought it was real".
Those are the most realistic CG effects because they completely fool the viewer.
So I'd say something like either the underground tubeway fight scene in The Matrix, because I just assumed that the environment that they were fighting is was completely real when I first watched it. It turned out the the entire environment which they were fighting in was actually a 3D computer generated environment.
Very impressive, you could watch it again right now and still swear that it was real.
And also the CG effects to recreate a fictional version of Manhattan, New York, in Spiderman.
I believe that some parts were real buildings which were mixed in with 3D computer graphic buildings, and were seamlessly blended together when Spiderman is swooping around swinging by his web amongst the New York skyline.
Outstanding CG effects.
The recreation of 1930's New York in King Kong, and the jungle itself, were also some of the best CG effects I've seen around recently.