Another vote for The Menagerie. The tribunal plot goes nowhere, and I have some issues with its implications.
Isn't that the point of the tribunal plot though? That it's meant to be going nowhere. In fact, it's meant to distract Kirk from trying to regain control of the Enterprise. To be honest though, my only issue with The Menagerie is that in hindsight it's too near to the start of the run and might have been better later on in the series. I know that would have been impractical as they had to recycle the footage from The Cage to make up a quick two-parter, and yes I also know that The Cage wouldn't have been seen at the time so it wouldn't have been fresh in anyone's memories.