DS9 is on right now at 12:14am and they are playing one of my favorite episodes of all time for DS9 - Duet. It’s the episode about a supposed Cardassian war criminal who is recognized by Kira. He desperately pushes and intimidates Kira and the rest of the Bajorans on the station so that he may be punished for war crimes.
Other favorites:
Crossover - Kira and Bashir end up in the alternate universe that Kirk once visited where there is no Federation.
Far Beyond the Stars - Sisko believes he is a 1950’s science fiction writer who writes about a black starship captain in the distant future.
Who Mourns for Morn - Morn dies and a lot of “old friends” come by, seeking to claim a fortune.
Wow, you mentioned several, but still managed to miss my own favorites:
The Visitor: The only one of those “time anomaly” episodes that really worked for me. Sisko gets lost in some kind of limbo, and we follow Jake through the rest of his life as he tries to retrieve him, finally succeeding as an old man…by taking his own life.
By the Pale Moonlight: Through a series of intrigues, Sisko gets Garak to help bring the Romulans into the war against the Dominion. Sisko violates all his higher principles to do so and destroys his self-respect…which Garak calls “a fair bargain.”
Rocks and Shoals: Several DS9 officers are stranded on a barren planet with a number of Jem-Hadar and their Vorta boss. The Vorta does something unspeakable to his men.
I like In the Pale Moonlight the best, and others not mentioned are:
House of Quark- Through an accident, Quark becomes head of a Klingon house.
The Magnificent Ferengi- Almost every Ferengi on DS9 appears in this episode, where they rescue Moogie from the Dominion (with Iggy Pop!)
A Call to Arms- Mining the wormhole, abandoning the station, and an ultra-cool Federation/Klingon fleetshot at the end.
Ones i didn’t like: Any bajor/prophet/pah wraith/Vedek/Kai/Winn/Bariel episode without a decent sub-plot, i refer to them as BBE’s (Boring Bajor Episodes).
The Siege of AR-558: The most affecting combat story ever done in a Star Trek series, with a memorably eerie battle scene. Also its semi-sequel, It’s Only A Paper Moon, dealing with Nog’s reaction to having been wounded in that battle.
Badda-Bing, Badda-Bang: I can’t help it: I love Vic Fontaine, and I loved that Trek’s producers opted to do an entire episode with no space battles, no interstellar politics and no Bajoran gods – simply an Ocean’s 11-style Vegas caper.
One Little Ship: The ultimate “bullshit Trek technobabble story,” turned on its ear and played for comedy.
Trials and Tribble-ations: For reasons that must surely be obvious.
Necessary Evil - Where Odo takes on an investigation that’s connected to the case in which he first met Kira, which we see in flashback. The ending is so powerful, and puts Odo and Kira’s relationship in a new light.
I also love the ending of Chimera (I think that’s the one) where Odo surrounds Kira with sparkling strands of himself to show his love for her.
In case you can’t tell, I’m a big Odo fan.
Most of the final 10-parter was amazing too. And I cried in the final episode. (Based on my comments above, I think you can guess when.)
Trials and Tribulations - great special effects and that whole Klingon forehead thing.
I can’t recall the title, but it was the episode in which the station was equipped with some kick-ass wepaonry. Great battle scenes.
My favorite is “Rocks and Shoals,” already mentioned by Fiver, who has excellent taste in DS9. And I think all my other favorites have been covered, too…
In the interest of time, I won’t second a lot of good choices here (nor will I castigate some awful choices). I will, however, quickly add Emissary, In the Hands of the Prophets, Defiant, The Adversary, Return to Grace, Hard Time, and Valiant. But only because you asked.
Most of the final season - the huge massed fleets, Federation attack fighters, starships weaving in and out of each other’s formations like F-16’s…thrilling.
Mine would have to be Far Beyond the Stars as well. Steven Barnes did the novelization of the episode, and, I have to admit, it was incredibly good. It went far more indepth than the ep could, and still managed to stay true to the cannon taht was the episode. I highly recommend it for anyone who liked the episode.
And I think all my other favorites have been covered, too…