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That's how Kirk defeated Kahn. He understood that space isn't limited to just 2 dimensions
I'm actually surprised you were the first person to bring that up. I was going to, but then I got into a conversation with someone in the thread and forgot. It's the only time I can remember where they really used the idea that space is three dimensional.
They even make a note of it that Khan is possible to defeat because of it. Spock says, "he is intelligent, but not experienced. His pattern indicates two dimensional thinking."
And then virtually all other Star Trek space battles are based on two dimensional thinking. Oh well.
There is no other battle shown in Star Trek to rival the time given to the one in Khan.
Off the top of my head there are incidences of ships being behind moons, in weird places they wouldn't expect, etc. It's just not a) discussed nearly as much on screen or b} shown on screen.
When we do see big battles, they are in 3d - Wolf 359 comes to mind.
I think you are correct that Khan is explicit and gives it a lot of punch, but I would argue we shouldn't be too quick to say they almost never deal with 3d/zero g.
(who remembers Klingon's blood is pink?)
Picard season 3 has a longer battle, and its a lot more 3d than previous shows.
DS9 did have a few battles take advantage of 3D space but not to the degree or time WoK gives it. Sisco using the mirror-verse Defiant against Mirror Worfs Neg'Vhar. Comes to mind, or how the Klingons in general would 'dive' onto Dominion ships from odd angles during set piece battles.