Season seven is my favorite year of DS9. It was firing on all cylinders. It gave us a little bit of everything from entertaining fluff pieces like "Badda Bing" and "Take Me Out to the Holosuite" and "The Emperor's New Cloak" to my favorite 10 part storyline with the Final Chapter which in no small way contributes to this being my favorite season of DS9.
Actually, I'd love nothing more than to include the Final Chapter as one of my favorite episodes since it really is just one big episode. I can't believe it has been 9 years since it was first run. I still remember how much fun I had for those two months watching it unfold. It was full of suspense as we anxiously awaited the ultimates fates of the various characters(both major and recurring). It had some of the best twists and bold moves I had seen up until that point. The surprise attack on San Francisco, the Breen joining the Dominion, Section 31 behind the Founders' disease, Odo infected, Kira donning a Starfleet uniform and helping Damar form a resistance, the Defiant's destruction. Where most of the characters ended up were satisfying and appropriate--Martok the new Klingon chancellor, Rom becoming the new kinder gentler Nagus for a new Ferenginar, Worf becoming an ambassador, Garak returning to home from exile only to witness the destruction of his world, Odo becoming the leader to the Founders to guide them towards a less xenophobic imperialist attitude, the ingenuis idea of pairing up Winn and Dukat.
I also really appreciated the way the writers took the time to not only focus on the characters but also on the familiar Trek species/civilizations like the Klingons, Cardassians, Ferengi by reflecting on them with the various meditations. And even though VOY was still going to be airing, it only added to the sense of melancholy that the show was wrapping up and for the time being things in the Alpha Quadrant were also coming to an end. I also loved how the writers brought the series full circle with the Bajor/Cardassian parallels. Making it even more impressive is the fact that this wasn't some carefully designed long term story mapped out from the beginning of the series. The writers pulled it off with a lot of luck as well as just being creative writers. And that could be applied to a lot of things in the final ten episodes. It is amazing to look back at how they managed to pull seven years worth of seemingly disconnected elements and threads and pull them together in satisfying and organic ways. Heck, we even saw the return of Mila!
I also really loved how Behr gave us a bunch of scenes with the Founder, Weyoun, Winn, Dukat, Damar, the Breen etc. I got a kick out of watching their plotting and perspectives. I still to this day find the Dominion to be one of the best "villians". I also loved the little touches like the Founder restoring her appearance before meeting with the Breen showing that they maybe "allies" but she doesn't trust them she is just using them, the Jem'Hadar glancing at Damar when discussing ith Weyoun about giving away Cardassian territory to the Breen, Winn's pleas to the prophets after realizing she has been duped by the Pagh'wraiths going unanswered because the Prophets being non-linear could see she was going to betray them irregardless of what they did.
But since I have to vote for individual episodes I'm going with
What You Leave Behind because it pulls all the threads together and is the climax.
Tacking into the Wind
Treachery Faith and the Great River--key episode setting up some of the elements for the Final Chapter with the revelation that the Founders are dying as well as some great work from Weyoun and I enjoyed the B-plot.
