Many great ones have already been mentioned: The destruction of the Odyssey, the introduction of the Defiant, the destruction of the joint Cardassian/Romulan fleet, DS9's sheer firepower come season 4, Odo killing one of his own, Martok as a Changeling, how bad "Let He Who is Without Sin" was, Bashir as a Changeling, Dukat turning on Sisko and crew, Starfleet giving up DS9, the Vedek committing suicide, the battle to retake DS9, Dukat spiraling into madness, basically all of ITPM, Dax's death (though it could have been handled better), the assassination attempt on Sisko, Nog losing his leg as well as "The Siege of AR-558" as a whole, Ross's actions in "Inter Arma Enim Silent Leges", the amazing development Damar went through, the unlikely alliance between Damar and Kira / Starfleet, seeing Dukat walk the corridors of DS9 undetected, and lots of other terrific stuff in the final arc.
To this I would add one element from "Emissary" that didn't awe me first time around because I didn't really understand what it meant. The Prophets reveal to Sisko that his existence is by no means linear. He's never really moved on from that point in time where he lost Jennifer.
It wasn't until a few years ago that I really understood what that meant, what they were saying, and that people can in fact live that way. They may age, their bodies may age but they don't move on inside and keep coming back to that defining moment.
It can be very, very hard to move away from that. For me, re-watching "Emissary" and understanding that, really, for the first time was startling and very powerful