Every time this question is asked, people always choose the usual suspects:
"Duet",
"In the Pale Moonlight", and
"The Visitor". I like them all, but I think the best DS9 episode should be one that showcase much of the cast.
"Duet" and
"The Visitor" are above all else great showcases for guest stars. The people guest starring in those episodes give thrilling performances, but one performance does not a classic episode make.
"In the Pale Moonlight" deserves a lot of praise for how original and surprising its plot was. It has a hell of an ending too, but again, that's just one thing - a really impressive plot.
I like
"Trials and Tribble-ations" most because it has both a very clever plot and wonderfully memorable performances from so many cast members. It pairs off a bunch of characters and has lovely interplay between all of them, and good interaction between characters is what I love best in Star Trek. The pairings of Jadzia and Sisko, Odo and Worf, and Bashir and O'Brien are all tremendous in that episode. Unfortunately it didn't give Kira, Quark, and Jake much to do so it's not perfect, but it certainly used the cast better than those mostly 'one-man show' episodes did.
Some have argued with me that
"Trials and Tribble-Ations" shouldn't be considered a possible best DS9 episode because it being an 'anniversary tribute' and pseudo-crossover with the the original series makes it less of a pure DS9 episode and I think that's a fair point. Ira Steven Behr himself said something like that, claiming he'd prefer the most beloved DS9 episode to be one that stands on its own merits, instead of one that partially benefits from feeding off the nostalgia and quality of an old Star Trek episode.
If I had to pick a best 'pure' episode, it would be
"To the Death", again because it's one that shows us some of the nicest examples of the family-like interaction between characters that are so endearing about Star Trek, it has really affecting character moments, and it's anchored by an original story (in this case, exploring the Jemhadar culture and how it comes into conflict with Starfleet).
As for the popular choices, I dig
"Call to Arms",
"Sacrifice of Angels", and
"Way of the Warrior" a lot too, because like some of what I consider the best TNG episodes (i.e.
"The Best of Both Worlds" and
"Yesterday's Enterprise"), they have epic action, but at the same time are down-to-earth and thoughtful enough to include emotionally involving explorations of character relationships. I can't share a lot of the popular opinions, though, because I'm a softie who likes some of the lighter, sweeter episodes like
"His Way",
"You Are Cordially Invited..." and
"Take Me Out to the Holosuite", while so many of you sickos prefer the more violent, morally controversial stuff.
