Star Trek has long been a series that challenged preconceived notions about life. Its entire stance as a show has been to challenge the viewer. To give the audience something to think about in bed as you fall off to sleep. For the most part, it's done a great job at doing just that. In fact, for many fans, it's the reason to watch Star Trek.
So it's really no surprise that one of the first episodes to ever do that would be the leading man's favorite episode. The episode, "The Devil in the Dark", centered around James Kirk, Spock, Leonard McCoy, and other crewmen heading down to the planet to investigate. They would find an alien creature, named The Horta, and would assume its hostility.
In actuality, all the creature was trying to do was protect its offspring. See, the Horta was a mother and had laid eggs waiting for them to hatch. Yet, its monstrous appearance caused everyone to react as if the creature was truly a threat. All because of it's appearance. It was a metaphor for many real-life scenarios where we may judge someone incorrectly, just because of how they look.
It was a compelling story. Yet, according to Shatner's autobiography (via ScreenRant), Shatner had a different reason for loving the episode. We talked before about how Shatner dealt with the passing of his father. His father's passing came during the filming of this specific episode. He filmed his scenes before leaving, but apparently Leonard Nimoy (Spock), decided to put a little gravy on his lines.
Apparently, Nimoy delivered his lines in a way done especially to make Shatner laugh. The gesture from one friend to another touched Shatner deeply. It's why he would pick this episode as his favorite. It'd be interesting to see if his thoughts and feelings have changed over the years.
While Shatner's reason for loving this episode is purely personal, it should be noted that it remains one of the tentpole episodes of the franchise. A standout story that personifies what Star Trek is all about. It tried to teach people that we're very similar, even if we may appear different. That's a life lesson many could embrace these days.