The Battle Royale at the finale is awesome (even if it is a little too goofy at times) and is still among the most iconic battles in Kaiju eiga and a turning point in the development of Godzilla himself.
The sequence where King Ghidorah devastates Tokyo is also great stuff, and makes very other scene of city destruction before it (and most after) look like a picnic- nothing has been quite as grand
And of course, Rodan vs Godzilla, where the pterosaur actually goes toe to toe with the King of the Monsters.
And when Mothra convinces them both to get their heads out of their asses and battle King Ghidorah.
King Ghidorah's first appearance: a huge fireball erupts out of a crashed meteor, then forms into the shape and solidifies: pure destruction made flesh. One of the most spectacular introductions of any monster in all of cinema.