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*
From Spock's World - McCoy vs. several Vulcans. The good doctor has surprising compassion (especially considering what happened the last time he was there), but he won't take any illogical anti-human guff off anyone and gets in some good jabs that are part insult and part calling out.
Also, the debate itself starts off with recurring character K's't'lk - a glass spider - going up against a snooty Vulcan (Bones tabs the Vulcan as "tenured") over the very nature of reality itself... which K's't'lk wins by biting that snooty Vulcan on the leg.
And Kirk overhears K's't'lk muttering to herself as she leaves "...that showed him. Get all Zen with ME..."
In one of her Star Trek novels someone mentioned the roller coaster. Chekov, for once telling the truth, stated it was originally invented in Russia... And nobody believed him.
Every time a Romulan encounters Naraht, for the first time. Why? Romulan religion worship elements... And Naraht, being a Horta, just looks like living Earth, pulling an accidental God Guise.
Naraht does it on purpose in The Romulan Way on the whole Romulan Empire: they were broadcasting McCoy alleged trial before the Senate when Naraht broke in.
In My Enemy, My Ally, Ael and the crew of the Enterprise are on a Rihan space station, and need to pass through a door that is too dense to penetrate with their weapons. Ael's solution? She had Naraht eat it.