I'm the same way with cues from "What Are Little Girls Made Of?" used in "Arena." The much used "Ruk Protect" for example.
There are several tracks from "Is There In Truth No Beauty" that I tend to associate with "Day of the Dove" quite a bit, especially the music used in "Dove" for the emotion-vampire (or whatever it's called).
There's also a track from "Amok Time" that was used in "Journey to Babel" for the scene where Amanda pleads with Spock in his quarters to help save Sarek's life that just works so beautifully in that scene.
Also, whenever they play the track from "The Corbomite Maneuver" where they first attempt to evade the cube, and then destroy it, I always think of Captain Christopher attempting to intercept the Enterprise
with his F-104.