My personal favourite from DS9 is "In The Pale Moonlight" - that show did moral ambiguity and a darker Trek universe better than STD could ever hope to. It also, rather unfortunately given the focus paid to them later, shows the utter pointlessness of Section 31 - Starfleet officers are more than capable of ruthless pragmatism when push comes to shove without needing a shadowy cabal of amoral operatives answerable to no-one. Of course, it helps when you have Elim Garak:
So good.
"That's why you came to me, isn't it Captain? Because you knew I could do those things that you weren't capable of doing. Well, it worked. And you'll get what you wanted: a war between the Romulans and the Dominion. And if your conscience is bothering you, you should soothe it with the knowledge that you may have just saved the entire Alpha Quadrant, and all it cost was the life of one Romulan senator, one criminal...and the self-respect of one Starfleet officer. I don't know about you, but I'd call that a bargain."
So good.