There are a number of really nice effects. I can't access the picture links from the office, so I don' know what's posted here. For some reason Trekcore is blocked. Yet Flickr isn't. Tell me, which one is more apt to have offensive pictures?
Anyway…
The Enterprise against the moon shot is very nice. I appreciated the reflection in the window, but I would have liked it more if you saw the image grow larger as they approached the ship.
The shot of the shuttle leaving Yosemite was really pretty.
When the God Beam leaves Sha'Ka'Rhee and passes in front of the Enterprise, that is fabulous. The Enterprise model is drifting to the side, really selling it.
I loved the look of the God Planet, with the swirling gasses, especially during the reveal after breaching the barrier. The final shot of the Enterprise and the BOP in orbit is also nice.
The BOP decloaking during the shuttlecraft run from Nimbus III is wicked, especially how it looks to burst out of the screen. Shots like these make up for some that don't quite make it.
Other practical effects done in camera that I liked were the meld scenes in the Observation Room. They were set up like a stage play and all the more theatrical for it. Whatever his ability (or lack thereof) as a writer, Shatner as director was really excellent. The rear projection starfield in the same scene is outstanding. The barrier gradually enlarges as they approach and it's blurry. I read that this was an accident, but it works logically and truly adds to the reality of the scene. Whenever Trek used rear projection for the viewscreens or windows, it made it very real. Unfortunately, it wasn't done nearly often enough. However, it doesn't always work…
Such as when Kirk falls off the mountain. The close up of Shatner calmly waving his arms and legs against the screen, with nothing to show wind resistence, is just laughable. It happens so early in the film, it's a downer. As far as less amazing model shots, sometimes it really did look like the Enterprise was a cut out slid across the screen. The shot of it going to warp and evading the torpedo shot should have been a fist in the air moment. But the graphic let it down and ended the sequence with a thud. There were others, but we all know 'em.