The winner for season 6 with 14 out of 31 votes (45.16%) is:
In the Pale Moonlight
Here's how it ends. SPOILER alert:
then, of course, there's this infamous scene...
Lots of interesting behind-the-scenes about this episode and the story writing process on Memory Alpha
. Here is a tidbit about how the show was received by fans:
• According to the Star Trek: Deep Space Nine Companion (p. 555), this episode is generally considered by both fans and staff as the darkest Star Trek episode ever made, and the one most antithetical to Gene Roddenberry's initial views of Starfleet, the Federation and 24th century Humanity.
• Despite this, the episode has proven one of the most popular among fans. When the series ended in 1999, a poll run in Sci-Fi Entertainment had this episode as the highest rated show of the entire seven year run, followed by "The Visitor" and "Far Beyond the Stars". Furthermore, this episode has an average rating of 4.8/5 on the official Star Trek website (as of October 14th, 2008), making it one of the highest rated episodes on the entire site.
• Andrew Robinson nominates this as one of his favorite episodes, after "The Wire", "Improbable Cause" and "The Die is Cast". According to Robinson, this episode is about Garak teaching Sisko that "You can't go to bed with the Devil without having sex." (Star Trek: Deep Space Nine Companion, p. 555)
• Of this episode, writer Michael Taylor says, "It showed how Deep Space Nine could really stretch the Star Trekformula. It pushes the boundaries in a realistic way, because the decisions Sisko makes are the kinds of decisions that have to be made in war. They're for the greater good." (Star Trek: Deep Space Nine Companion, p. 556)
• In a separate interview, Robinson made a similar point, stating that this episode demonstrated how Deep Space Nine explored more difficult issues than the other Star Trek series. He commented, "[B]asically it exposes the American innocence, that we want to do these things in the world, but we're not really willing to take the consequences of our actions, and sometimes we have to do very dirty things, and we have to hurt people, and we pretend that that doesn't exist, that Americans would never do that. We dealt with issues like that and I don't think... you know... the other shows really went as far as we did."