I think that one of the reasons that Khan fairs so well in the Star Trek movie countdown is that there are only 11 movies, including the newest one. That's not a lot to choose from. When you've only got 11 films from which to pick, there's just not much debate about which of those 11 is going to be the best. Does Khan have plot holes? yeah...sure it does. Are there special effects problems? sure. Character issues? You betcha!
Would you say that Khan is among the greatest movies of all time, in general? No, probably not (there was at least one person in this thread that did say it was their favorite movie of all time). Compared to Citizen Kane, Casablanca, etc, it's not that great but compared to only the other 10 Star Trek films? It's a pretty impressive bit of cinema!
Don't get me wrong here. I love Star Trek and I find good things in all of the films. I include V and X in that. I liked all of them for what they were and i would tend to agree that II is pretty high up in the list of "best Star Trek movies".
If you think about it, if you were to create a list of the "Top Ten Star Trek Movies ever", you'd only be leaving ONE MOVIE off that list...and it wouldn't be Khan regardless of the plot holes, character issues, illogical actions of the crew, etc.