And I have a few things to comment on. SPOILERS if you never saw the show or the final season!
1) Loved the Dominion War finale: PEW PEW PEW LASER GUNS! SHIPS! EXPLOSIONS! And the Cardies switch sides!
2) The whole Cardassian revolution: well played, Damar as a character really shines, and I love the whole nervous laughter bit outside Dominion HQ... and Damar exits heroically, with Garak picking up the leadership role
3) The Klingons: Martok and Worf are a great Klingon duo, and JG Hertzler played Martok to perfection. Great bit of Worf taking on Gowron.
4) The O'Brien/Bashir subplot: taking on Section 31 to save Odo, fighting in the Alamo battle in the holosuite, playing darts, drinking together, and ultimately parting ways.
5) Odo and Kira: You really feel for both of them, and Nana Visitor really upped her game for the final season, and played Kira in new and excellent ways. Very touching end to their time together too.
6) The quick Ferengi plot thread: Rom becoming Nagus, Quark railing against the changing Ferengi society, and Nog growing as a person and as a Starfleet officer.
7) The camaraderie of the main cast on the bridge of the Defiant. I love the banter between all of them, especially in the last few episodes.
8) Garak: His character arc ends nicely, without ever compromising who he has been the entire series. He also gets to toast Weyoun, which was a bonus.
1) The Great Link, and the Founders plot thread resolution: it was all just a little too tidy, regardless of the Odo/Kira emotional aspect of it.
2) the Ezri/Bashir romance. I dunno... it could have been better. It wasn't bad, but at times it did annoy me. The Ezri character in general was hit-or-miss for me. When she was good, she was great, but when she wasn't, well... bleh.
1) The whole Pah-Wraiths stupidity: god, I never liked Winn (though I liek the actress who plays her), and Dukat became almost comical as a pseudo-Bajoran. The "final battle" between Dukat and Sisko is incredibly anti-climactic, and the whole subplot was overall painful to watch. I sometimes felt like the show runners didn't know what to do with Dukat. He's a Cardassian captain. NO, he's a ruthless dictator. NO, he's a evil religious zealot... NO wait, he's... blahblahblah....
2) Sisko as the Emissary: I got tired of how the Prophets kept screwing with his life, and how he just up and leaves preggers Cassidy and Jake and everyone at the end.
Overall, I was choked up as the final episode wrapped up: the whole gang in the holosuite with Vic, everything changing, but the station soldiering on (unless you read the novels, but... well, ain't gonna spoil that...)