It's gotta be City On The Edge of Forever.
Seriously, before I even saw your choices, I immediately thought of "Star Trek V: The Final Frontier." Without a doubt it's the worst representation of Star Trek I can think of. I don't know if it's all William Shatner's fault (as director), or if other forces got in the way. But it's a piece of Trek history I'd rather forget.
Spock's Brain was out there, but I'd rather watch that five times in a row than claim any creative input on Final Frontier.
I thought Nemesis was alright, and Star Trek: The Motion Picture--though long and very tedious at times--was a wonderful rebirth of Trek which I'll never forget. Looking back, the actors all looked so young. And the story was really quite good. It just got lost in the editing or direction, or maybe in someone's desperate desire to dazzle the audience with visual effects more than recapture the feel of the series. There are things I don't like about it, but it has a special place in my heart.
I confess I don't know the others you named (though I may have seen them).
Hmm... I just thought of one you didn't name, which overall I find mind-numbingly dull: Return To Tomorrow, from the original series, in which alien beings Sargon, Thalassa, and Henoch inhabit the bodies of Kirk, Dr. Ann Mulhall, and Spock. It had its moments, and was actually a sweet story, I suppose. But it just seems to drag. Given a choice between that episode and some of today's pitiful sci-fi, I'll still take Trek. But it's not the brightest spot in Gene Roddenberry's universe.