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I think "The Visitor" is the best DS9 episode just because of the emotion and bond you see between Jake and Sisko.

But I think the best DS9 episode that isn't focused on father/son would be "In the Pale Moonlight" where Sisko basically has an official assassinated in order to get enemies to enter the war against the Dominion. In his mind, it had to be done for the greater good.

You really get a sense of how dark, dangerous and desperate the galaxy had become and really, that's what DS9 was all about - showing the gritty underbelly of the Star Trek universe.