1. Star Trek VI - The Undiscovered Country - Wild card, I watched this with my dad, so it's my overall favorite for personal reasons. I'll defer to others on whether it really belongs at #1.
2. First Contact - Viola Davis is a national treasure and her performance elevates this film.
3. Voyage Home - The OG cast performing in peak conditions.
4. Wrath of Khan - It's ricidulous to put this masterpiece this low on my list. I'm sorry, and I will rethink my life.
5. Generations - Has a little is everything. I probably rank it higher because it is a celebration of Trek history. But that said, for the number of cast and cameos, this is a surprisingly great movie.
6. 09 Yes, it's a popcorn blockbuster, but Chris Helmsworth's opening scene is a masterful performance, and plenty of solid Star Trek follows. Zoe Saldana is a national treasure and elevates this movie. Leonard Nimoy delivers another fantastic performance.
7. Beyond - The Yorktown is one of the coolest things I've seen in scifi, and the movie is solid.
8. Nemesis - An important chapter in Brent Spiner's decades long perfected Pinochio story.
9. Into darkness - Zoe Saldana is a national treasure and is unfortunately not in the remaining films in my list. I'm saying this tongue-in-cheek since plenty of Trek actors deserve highlighted here.

After this point, I really like the remaining films, but not enough to have strong feelings to rank them.

10-12) Search, Insurrection, Final Frontier

...

13. The Motion Picture - Still a pretty great film, but the pacing issues prevent me from rewatching it often.