Mirror, Mirror comes as a close second, but my issue with it is how quickly Kirk formulates the theory of being in a parallel universe. Those lines kind of felt like artificially put there to make the watcher understand exactly what is happening.
What other theories should Kirk have considered, that fit the facts as they knew them at that point?
I second this, really there wasn't any other option Kirk could have considered, apart from maybe Spock went nuts and changed everything around while he was on the planet!
I loved the DS9 Mirror Universe episodes, but as a fun distraction rather than a "true" mirror universe story, I could even postulate that they may be in a "different" mirror universe to that shown in Mirror, Mirror and In A Mirror Darkly.
I regard the latter two as fantastic episodes. I always thought it would have been fun for TOS to re-visit the universe, discovering that Kor was almost like Kirk, with the Klingons and Romulans being very Federation-like.