Quite a few - Duane is the sort of writer who can sneak up on you and leave you gasping for breath. The acme of all these moments, though, has to be when Kirk finally gets fed up with McCoy's kvetching and puts him in command of the Enterprise in Doctor's Orders.
Dark Mirror: The whacked-out improv opera at the end.
Related to this, Worf's line about a particular Klingon opera: "There was fighting in the streets for three days, and the government fell. And then-" *interruption ensues*
In The Wounded Sky Kirk barely gets out of the way before K't'lk charges through the door - "an effect like almost being run over by a xylophone." Apparently Hamalki jingle when they move.