2. Star Trek VI: The Undiscovered Country
Personally, this film had a larger impact on the Star Trek narrative than Wrath of Khan, and more importantly, I feel the Klingon captain Chang was a far better villain than Khan. Despite being a super genius, Khan's whole plan was a chance encounter. They highjacked a Federation ship and had their teeth kicked down their throats by Kirk and the Enterprise. Khan didn't even kill Spock, originally. Spock died as an inadvertent side effect of Khan. And then he was resurrected. Chang singlehandedly killed off his superiors, blamed James Kirk and nearly ended the famed captain in an epic space battle. Truly the second-best villain of the franchise, and one who should be far more respected due to his near-perfect attempt to stage a coup against the Klingon empire.
1. Star Trek: First Contact
In my honest opinion, the best Star Trek film in the franchise's history. It featured the series' best Star Trek villains, the Borg, it finished the Borg and Picard storyline in a satisfying way (before the Picard series undid that) and it brought in aspects of Star Trek: Deep Space Nine. Not only that but it served not only as a true sequel to Star Trek: The Next Generation but also as a franchise prequel, highlighting the first time that Vulcans and humanity met in earnest. It's not only a perfect Star Trek film but a perfect film period. It also introduced one of the coolest villains ever, The Borg Queen. Combining a hot series in Deep Space Nine, with a storyline continued from The Next Generation, while serving as a direct sequel to that show, while also being a franchise prequel, and an S-tier villain makes this the defacto best film.