My faves have always been:
1. The Wrath of Khan-outstanding script, direction and acting. Not to mention Montalban's muscular chest! Wow!
2. The Search for Spock- for "Stealing the Enterprise" scene, Spock/Kirk "You came back for me" speech and performance by Mark Leonard as Sarek.
3. The Voyage Home - for "Punk on the Bus" scene, outstanding performance by De Kelley for "Chekov rescue scene" and enviromental message. Good script and direction.
4. The Motion Picture - Fond memories because it was the first Star Trek since TV series....hey, we were hungry in those days!
5. The Final Frontier- Enjoyable opening sequence in Yellowstone, good performance by Lawrence Luckinbill.
6. Insurrection - Like a good TNG TV episode.
7. The Undiscovered Country - Poor direction and pacing. Performances inconsistant. Pepto-Bismal Blood of Klingon unbelievable. Mind rape of Valaris disturbing.
8. Generations - Poor direction and plotting. Script nonsensical. Cast not taking their performances seriously. Killing of Kirk wrong. Outstanding performance by Malcolm McDowell.
9 and 10. First Contact & Nemesis - So bad I couldn't sit through them to the end. Poor direction and inconsistant plotting. Cast not taking roles seriously.
11. Star Trek 2009 - Not Star Trek in my opinion. Sorry, my gut won't allow any other answer.