Khan is a great movie and my second best for a reason. But as I've stated before, Trek has a feel that Voyage just captured for me more than any of the others. The characters being fishes out of water, so to speak, and the fact that Spock let each character really have a scene or two to shine, made it the movie that felt most like Trek to me. And they were allowed to really play up the humor, which was a really big part of the appeal of the original series.
In terms of the larger Trek mythos, however, Khan is clearly the superior movie. The way it brought back a choice Kirk made in the series and the consequences of that choice playing out on the big screen made it an really good movie, no less so for coming after the cerebrally-interesting and cinematically-snooze-inducing first movie. Spock's dying felt earned and tragic, even though every time I see Shatner giving his "the most............human." speech I can't help but crack up. I loved Nimoy finally getting to do the "these are the voyages" as the ship sails away.
Yet in an effort to avoid getting scolded for straying into the wrong fictional universe, let me get back on topic: Star Wars is a thing. Discuss.