In retrospect, I agree that this should have been broken out into two distinct categories: All out comedy, and funny elements. Oh well...
I also think that the 2nd season tried to inject too many gag moments, some that seemed out of place for the "spirit" of the episodes.
Yeah, "Plato's Stepchildren" was more funny-odd, really. Especially when Shatner is crawling on all fours with Alexander on his back. It must have been seriously embarrassing to perform it. I'd bet anything that Shatner put up some resistance to going along with it. Out of context, it's hilarious to see. That's why I put it in the list... but it's certainly not a favorite episode of mine. The writers should have taken more liberties with Shakespeare and had the crew performing acts from a variety of plays, maybe the "funniest of" in Shakespeare. It would have at least made the episode more palatable.
I'm kind of surprised that none of the DVD releases ever compiled a "funniest moments" montage as an added bonus.