Booby trap and Yesterday’s enterprise are truly where 3 graduates, plus BoBW obviously.
But I actually liked Sins of the Father, it completely rewrote the concept of Klingons, this is the episode that took them from “evil alien stand-in antagonists” to “race with actual character traits and motivations beyond ‘KILL!’”.
Tin Man too, and the Defector, they both added the Romulans in with more flavor, S3 was actually Romulan heavy even if they weren’t onscreen for most of their action (The Enemy had one on screen but not… doing anything).