Optimus turning the tide in TFTM will always be hard to beat.

The Hot Rod vs Galvatron fight from the end of TFTM too is a good example of Transformers transforming back and forth during battle, both using both modes for tactical advantage. There should be more like this, but it tends to be too rare sadly.

I quite liked the Autobots vs the Dreads in DOTM.

Blackarachnia vs Inferno in "Other Voices" was a lot of fun at the time.

And it's not quite a battle since Waspinator never stood a chance, but when Rhinox pulls out the Chaingun of Doom for the first time in "Chain of Command" it's still awesome.