Elim Garak, because how can you not love a patently duplicitous and yet still somehow generally benevolent smooth-talker who chews all the scenery and exudes the queerest energy simple tailor?
It's a basic ass answer but Sisko. Star Trek has tried moral compromise a lot by now, but Sisko remains the only one where it really hit for me. Later Trek, where it's more common, just doesn't have the same level of professionalism or idealism for it to feel meaningful.
In a world of "humanoid/android/AI/chair/lawnmower explores what it means to be human" it was very refreshing to see "human raised as not-human explores what it means to be human."
Dukat. I don't like him a person, but he's a great character. No other Trek character has ever been written as richly or layeredly as he.
At first you assume he's your basic racist bent on hatred and power. Then you realize his obsession with Kira isn't just about destroying an enemy, but his secret love-hate for Bajoran women. We meet Ziyal whom he mostly loves, but is ashamed of. He goes mad, starts a cult, makes himself appear Bajoran and starts a relationship with Kai Winn (ostensibly with other motives, but I think he reveled in it), and ultimately dies for and in his mad faith.
DS9 is lower on my list when I rank the various series, but some of the characters, and defininitely Dukat, top the list of characters.