1 is Wrath of Khan. Who doesnt like a good battle in space by these ships? Not to mention the death and ceremony of Spocks death was very emtional.
2 is the search for spock. It really brought a tear and amazment to see the Enterprise blow up as it did. You wont be seeing anything like that in any series or movies. I know for I have looked. the closest is from Star Trek Legacy if you blow it up.
the 3rd is the new movie. Yes it had its down sides but the running joke of "I'm gona throw up on you" and the numrious times Kirk showed bad reactions was too funny.
Now I know that your free shuttle is done and gone, but I had one more thing I think counts kinda like a Kligon proverb to the other guys answere. To be. Or not. To be.
First Contact! Everything from the music to the writing is excellent. One of the best sci-fi movies ever!
Yes and no. A guy on youtube took the time to make a video on all the errors that were made, mostly from the cast of the next generation. Like how Picard said there was only 32 decks on the Enterprise E, then where did deck 56 come from?