Its hard to choose, because I love the dominion story that took over. I also appreciated the stand alone episodes. The Dominion was not all that deep space nine was- But it was the Dominion Arc that grabbed a lot of viewers and my imagination. I think therefore I have to choose a Dominion themed episode and that would be The Jem'Hadar, just simply because it introduced the best enemy ever. Also it was funny and finally gave the wormhole some purpose. I love ITPM and it is a Dominion story but its more about Starfleet and morals than the War itself so its a close second as a non Dominion Arc story. Sacrifice of Angles is a tie with ITPM.
Anything with Vic Fontaine sucks- well the parts with him in it at least. But not as bad as Fair Haven. Little green men was a brilliant take on Roswell.