I noticed the CGI less in this movie than any other FX-heavy film I've seen. The only obvious use of CGI that I noticed, was when they went into a close-up of the red matter as it imploded after the Jellyfish had crashed into Nero's ship.
The Enterprise itself was particularly stunning. Especially in the scene where the shuttle leaves Iowa with Kirk & Bones on board and they fly past the half-finished Enterprise. But everything was so well done. This is the way CGI should be used, as opposed to something like 'The Clone Wars' where it takes over the film.