Top 5 though in no particular order:
Kira Nerys: Probably the character who evolved the most in DS9, I think she only started really changing after the episode Duet. She starts off as a fighter and a thoroughly unwomanly woman with her hands-on-approach, hatred of the Cardassians and distrust of any non-Bajoran. But how she finds peace with herself is one very rewarding story arc, along with the bumps along the way.
Dukat: Dukat is so amazing because he is the perfect villain, he deludes himself into thinking his actions were correct or necessary (much like today's villains), and he can go from someone who ordered the deaths of a few thousand people to a passionate lover or caring father. Yet always that controlling element is always with him.
Kai Winn: Virtually every scene with Kai Winn makes me want to strangle her as she is so condescending and repugnant. She's sort of like the religious version of Dukat, and just like him she lies through her teeth about certain matters.
Odo: I like Odo's bravery and strong will, many a time life is not easy for him what with being estranged from his people and yet he continues on, I think he is the most resilient character in all of Star Trek.
O'Brien: O'Brien is probably the most believable character of all in DS9, he is always in character and though he doesn't undergo great changes like some of the other main characters did, his consistency is always endearing.