Watched "City..." on the Blu-ray last night. Wasn't much for the CGI guys to do but the ship in the opening, and a couple of planet shots.
But I have to comment on Nimoy's makeup. I guess the remastering process spikes the colors a bit. In a couple of early scenes Spock actually looked GREEN, and I could clearly see the makeup line around his neck. I guess this falls under the heading of "things they didn't think would show on 60s TV that hi-def doesn't do any favors for."
There are a number of subtle effects enhancements in the episode - they clean up the matte lines around the images on the tricorder, and during the end credits, where in the original the image of the Guardian (with its spilling vapor) "froze" during every title card they fixed it so that it remains moving.
You can see comparison images here: http://trekmovie.com/2006/10/12/review-city-on-the-edge-of-forever-remastered/ and a video of the new effects below:
[yt]http://www.youtube.com/watch?v=t6PrHmyDt14[/yt]