D'OH! Another, very hard season for me to choose favorite episodes from, though not as hard as with the previous one. The six, or seven if you want, episode arc is fantastic. But, I think I'll choose to list my favorite stand-alone episodes, as I should.
Far Beyond The Stars - Season 6's best episode, though not by much
Inquisition
In the Pale Moonlight
Far Beyond The Stars is just about the best directed Trek episode from a Trek actor, a perhaps the most honest science fiction story. Its a tribute to the genre, and its a tribute to Roddenberry and Fontana and Gene Coon and Issac Asimov all those guys that really gave a damn about science fiction, and also about the black people and stuff. Its not an episode I originally liked, mind you, but it has definitely grown on me.
Inquisition and In the Pale Moonlight as among the darkest Trek episodes ever, but they are filled with excellent writing, acting and directing, making them also very worthwhile. Michael Dorn (who also did last poll's celebrated In the Cards) surpassed himself with Inquisition, that also introduced Section 31. And In the Pale Moonlight is just the proof, that Sisko is one of the most interesting characters in the entire Trek canon. A really great story that reached into the darkest desperations of a man who wants an end for this bloody war. Its unlike anything Trek had ever handled before, and its a masterpiece as it is.
Great season, great episodes, all and all.... Except for Profit and Lace! God forbid..