There are so many... and some I can't recall the titles too since I'm tipsy but:
In the Pale Moonlight (sort of universal isn't it?)
Siege of Ar558 (something about it that is just so poignant)
The Visitor (just a nice personal episode)
Explorers (the one eppie that really got me into this series. I was overseas and this was that one that made me so mad I couldn't see it regularly)
And so many Klingon centric eppies... Sons of MOgh is a standout as well as Worf getting a place in the House of Martok.
It's just really hard to narrow this series down like this since there are only one or two "not as great" eppies. I mean, there isn't one episode I'd say is unwatchable or below the standard of almost any other television show. In fact, only two other series hold that distinction where even the "worst" episode is better than many other series period: MASH and Chuck. DS9 is just one of those special series.