Late to the party, but hey, I've been travelling over the Holidays...For me...
1. The Undiscovered Country - Best by far. For a Sci-Fi Mystery Thriller it's great...probably because there are not many of these out there. It's unique because of that and makes it so that it's an original take rather than a rehash of what we've seen in other science fiction films and such. It has a great send off and conclusion for the crew and ship, and you get to see the fulfillment of where and how many of them end up (Sulu as a Captain of his own ship, Spock as his own thing, the others vying for retirement, etc).
2. Wrath of Kahn - This one is many people's favorite for a reason (as shown in this thread). Among younger generations it doesn't have AS much appeal, though it still ranks at the top for many. There is a part of nostalgia that movtivates some to love this one so much while they miss a few of the more 'dated' flaws with it, or at least what some may assume are plot holes (tell me again...where was Chekov when they found Kahn in the original Space Seed???).
3. The Voyage Home - and talking of plot holes...this one comes with them aplenty. That said...This is just a fun movie with a fun soundtrack. I just enjoy it.
4. Search for Spock - This one seems to repeat itself occasionally. I can understand why they have the repeat at the beginning because it was a few years between #2's release and this one, but if you had just seen #2 or saw it a lot, it's just repetition. Then, once again you have repetition occur when they replay the death of Spock. It seems to...devalue it in some way. It lessens the impact when you see it over...and over on rewind, etc. I think that's part of why it doesn't rank as highly as #2.
#5 - The Final Frontier - Yes, I rank it higher than the Motion Picture as I'll note below. This one is just fun if you don't think too hard about it. I'm not sure HOW it matches up to Star Trek Canon otherwise (isn't earth on the edge of the Milky Way? So getting to the center of the galaxy took how long? And then you have Voyager which was cast to the other side of the Galaxy. If it would take them 80 years at maximum warp...shouldn't that mean it took 40 years...or something like that for the Enterprise to get to the center of the galaxy???).
#6 - This has my favorite scene in all of the movies. The opening sequence with the Klingons is just...perfect. So why so low on this list? Have you ever seen this movie? Then watched the director's cut? This movie is BORING! They take so much pride in their special effects that it seems to take forever! Cut this movie down to about an hour and you'd have a GREAT film. As it is...they stretch out a 45 minute movie into over 2 hours.
PS: No, it's not in the original directive of 1-6, so...
4a - Star Trek: Generations - So, not fully a ToS movie...I know it, you know it...and yet...there it is. It has Kirk, Chekov, and Scotty...and A Sulu. The part with the old TOS crew is actually pretty decent. I'd rank it akin to Search for Spock. It's fun, witty, and exciting. Too short. The rest doesn't fall under the ToS though, so only that part can be talked about.