S7 is my personal favorite. I think it's the most consistent of the seasons, closely followed by S5. It's the culmination of 6 years of build-up to, and it really pays off. The final chapter, in particular, is very powerful, I think. Granted, it's not without its flaws.
S6 would be next on my list. Its greatest episodes are truly excellent but it's got some pacing problems and some real clunkers in between that stick out like sore thumbs.
S4 comes after that for me. It's head and shoulders above the seasons before it IMHO and also the point where DS9 really, really took off, I think. It's actually quite consistent as well but not as excellent IMHO as the seasons after it. The Visitor remains my favorite episode to this day though, mind you.
Finally, it's season S2 followed by S3 and then S1. Don't get me wrong. I like DS9 from start to finish, not just the last four seasons. I just don't feel these seasons are quite as strong. I do think they have some great material however.
S2 is a consistently great season, I think, with only a few minor missteps. I would have liked to have seen a little more follow-up to the events in the opening three parter, however.
S3 has some excellent material, but I feel it's marred by quite a few clunkers and some uneasy setup (The Search sets up a lot that's forgotten later as well as resetting itself which I didn't mind at the time but which bothers me now).
S1 has one of DS9's finest episodes in general, I think. No, not Duet, Emissary. While I think that Duet is a great episode and very strong for a first season, Emissary is one of those few 'special' episodes. It does all the setup needed for the show while being entertaining and thought-provoking at the same time. It really, really milks the science fiction setting for what it's worth and uses it to effectively tell the story of Ben Sisko or many people in the real world, for that matter.
However, while S1 starts really strong and also ends on a strong note, it falters inbetween. There are some really good episodes like Progress which do an effective job of characterizing Bajor and its problems. But there's also a lot of standard Trek material that really added nothing to the specifics of DS9 and, as a consequence, came off relatively weak, I think.