Season 6 had a lot of great episodes to choose from as well.
I always thought Far Beyond the Stars was just... way out of place . A great message but one that kinda derails from the whole Star Trek setting. I get the sense Brooks probably pushed this one, which hey... star demands happen. At least he didn't ask to drive a dune buggy like Stewart did in Nemesis.
Anyways, my vote goes to In the Pale Moonlight. The first person narrative of Sisko really carries this episode. You can see how a normally good person can start down the slippery slope of morality. This episode really captures the grim situation of the war and Garak is just masterful in doing this thing in thoroughly manipulating everyone in his own unique style. Irony points for Sisko ripping into Dukat for some of the same things he did, and same justifications he did, a few episodes in Waltz.
Honorable mentions go to You are Cordially Invited, the Magnificent Ferengi and Who Mourns for Morn? for some fun, light hearted episodes among the otherwise grim story arc and for the six part epic from A time to Stand to Sacrifice of Angels, which the collective whole was greater than the sum of it's parts.