Lets see. Been a while since I've been able to catch Star Trek, but, I just have favorites from the series.
TOS:
Mirror, Mirror
TNG:
Best of Both Worlds Pts. I & II
DS9:
Our Man Bashir
(I'm a James Bond fan, so that cracked me up)
VOY:
Year of Hell Pts. I & II
(Though Endgame and Scorpion were close)
Though, I have to admit that I get a good laugh out of the episodes with Q in them. And I never watched an episode of Enterprise all the way through. Good concept, poor execution.
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Lieutenant Nicholas Tyler
Chief of Security, Starbase 34