I'm going to go with Tacking Into the Wind. Really a hard choice since I liked so many others this season, especially Faith, Treachery and the Great River, but this really struck me as a powerful episode on so many levels. The acting was great and every character was going through something quite dramatic. Bashir and O'brien were desperately searching for a cure to save Odo. Odo was trying to hide how bad it was from Kira, who knew anyways and was letting him delude himself to keep his self respect. Garak promised Odo he wouldn't tell, but did anyways but for once wasn't lying for the sake of just lying. Weyoun finally seemed to be falling out of favor with the Founder and Damar realized just how evil he and Cardassia had been his whole life and when the choice was put forth to him, literally with one pull of the trigger, choose to be a better man.
I just loved all of it. Not to mention Garak stepping out of the shadows with that creepy smile on his face makes a great avatar.