I agree with the sentiment of TMP having the fewest plot holes. It makes perfect sense to me that VGer would never want to wipe the old name off. It wanted to know more about its own origins.
Most plot holes would go to Nemesis, because to me, Shinzon was one giant walking plot hole. I never bought for one moment that he was Picard's clone, nor did I ever believe that the Romulans would just roll over and agree to make this human/Reman Praetor after a terrorist attack.
All the films have plot holes but one of my pet peeves has to do with Wrath of Khan. Ar the end of Space Seed, we see that Khan was marooned with his crew -- who are all ADULTS approximately Khan's own age. In WOK, which takes place 15 years later, Khan is surrounded entirely by 20-somethings, with not one adult in sight. So ALL of the adults died, except for Khan? And I guess before they died the Augments had a lot of babies in the first couple of years and Augment children just grow up really really fast?
I know they wanted to set Khan up as a mirror of Kirk, who was surrounded by a young crew, but this was just stupid. And the Ceti Alpha 5/6 confusion was stupid, too. Seriously, they don't bother to count the planets?