I'm with most people who mentioned episodes like "The Way to Eden", "Spectre of A Gun, ""The Royale" and "Move Along Home". I love most of those and while I'm certainly able to see why some could dislike them, I always enjoy rewatching them.
Another "episode" that is somewhat unjustly hated, I think, is "Shades of Gray", which – as clip shows go – isn't nearly as horrendous as most people are making it out to be.
Not an episode, but personally I will never ever get the hate directed at Keiko and her marriage with Miles O'Brien. The distaste so many people around here feel for their story is something I just cannot grasp, as I love them both and find their relationship to be the most realistic of the whole franchise.