According to one of the documentaries, director Robert Wise pulled a trick from George Lucas' playbook and re-did a few scenes, employing the use of CGI and other technologies. However, unlike Lucas, Wise set some restrictions on how to do it. He didn't want these re-done scenes to be distracting, so he asked the effects guys to limit the scenes to only reflect technology that was available in 1979. So no dewbacks walking around in the background.

He pulled it off nicely. The cheap matte paintings on Vulcan were replaced with more breathtaking scenery. There were a few new exterior Enterprise and V'Ger shots (we even get a few good looks at the V'Ger ship itself). And the hexagonal rocks are now seen extending out toward the Enterprise as the crew walks on the saucer.
There's a documentary covering the abandoned Star Trek: Phase II series, complete with bad hair and costumes. The actor who would have replaced Spock in the series (Nimoy wasn't interested) was given a small role in TMP as a scientist on space station Epsilon 9.
The commentary isn't the best, but it's interesting to hear the late Jerry Goldsmith chime in.
The overture and main titles have been modified. Instead of a plain black background, they now appear over a moving starfield.
Long before Peter Jackson used it, Robert Wise employed "forced perspective" in at least one scene. The engine room had a five-foot actor and a 3-foot boy dressed in engineer's uniforms standing next to the horizontal warp shaft, which was designed in such a way as to make it look longer than it really was.
Although the original MPAA rating was G, the DVD is rated PG. Makes more sense, since there are a few mild swear words and some light violence. Oh yeah... and McCoy with that beard and gold medallion is just obscene!
The DVD also features the trailers and TV commercials for the movie. The first two theatrical trailers are filled with cheesy '70s graphics. Kinda fun to watch.
Overall, the movie just went from 5/10 to 6.5/10.