Wrath of Khan
Undiscovered Country
Voyage Home
First Contact
Search for Spock
The others almost don't warrant rating. I don't include the reboot, because I think it's an apples and oranges comparison. If I did, it would still be middle of the list.
Wrath of Khan was just so...smart. So quotable, so well-shot, so well-acted. It was that near-perfect film that comes around once every few years. If Ricardo Montalban and William Shatner ever needed an epitaph, that film would be it. Both actors at the very peak of their abilities, two characters at such a crossroads in their lives: Kirk and his midlife crisis, Khan and his self-destructive desire for vengeance.
However, I still cannot watch the final ten minutes of the film without being brought to tears. That look on Kirk's face as the camera pans out from the engine room...such devastation, you really know his world has just completely shattered.