I'm really surprised more people haven't listed
"Star Trek II: The Wrath of Khan",
"Star Trek IV: The Voyage Home", and
"Star Trek: First Contact" as their favourites. Are Siskel and Ebert the only people who agree with me that these three are by far the best of the series? They are the only ones I own and the only ones that I think are pretty much perfect that I can watch over and over again and still find new reasons to love every time.
I'm a little disappointed by the special effects at the end of
"Star Trek II" and I think the first and third acts of
"Star Trek IV" aren't as strong as the middle act (the stuff in the past), but these are the only Star Trek movies that I find endlessly endearing, entertaining, and exciting! Wow, that's a lot of "Es"...I didn't even do that on purpose.
For me, the others are way too flawed. They all suffer from one of or all of the following: poorly-written characters, excruciatingly long stretches of boringness, and irritatingly clunky story lines. I do love parts of almost every Star Trek movie, except Insurrection, Nemesis, and The Final Frontier (only because I barely remember it), but those three I listed are the only ones that I think maintain a consistent high quality in writing, acting, and direction from start to finish.