I don't like either "City on the Edge of Forever" or "In the Pale Moonlight" because I disagree with the ideologies behind them. I don't like that "City" is an anti-pacifism story, though I concede that the issue is complicated, given the specific aspect of history the episode is dealing with. Buy my dislike of "In the Pale Moonlight" goes beyond my rejection of its anything-goes-in-war message. I just don't think it's all that artful and engaging, and I think the device of Sisko's narration is clumsily applied.
I don't know if "Dark Frontier" or "Future's End" are widely loved, but they're the kind of big cinematic adventures that seem to want to be widely loved, and I'm not much impressed with either.
Of the movies, I can't stand First Contact. The Picard and Lily stuff is okay, though I find the action sequences dull. But I hate how they turn Cochrane into a buffoon, and the stuff with Data and the Borg Queen seems like the titillated fantasy of a thirteen year-old sci fi fan building a robot in the garage.