The first encounter between Optimus Prime and Megatron.
Try Micron Legend's version. (Need new links).
And the last one tops this.
Optimus and Galvatron's duel at the end of Armada. Badassery in its purest form.
The time that Megatron shot Smokescreen with the Requiem Blaster, blasting him halfway through the wall and leaving a smoking, melting hole right through his abdomen. And then Smokescreen got up and attacked him again.
Starscream's suicide-by-Galvatron is probably a crowning moment of Tear Jerker as well. In a last-ditch attempt to make him see the threat of Unicron he goes up against Galvatron and the powerful Star Saber with nothing but his own sword; standing up to him literally and metaphorically for the first time in the series. And then he lets Galvatron impale him just to make a point.
Armada had a lot of flaws, but 'Cramp' is one of the best episodes in the history of the franchise, and it all rests on Starscream's shoulders. He fires into the sky against a PLANET-SIZED GOD-TRANSFORMER THAT EATS PLANETS, screaming: 'You're all mine, Unicron!'. It's a brilliant moment for one of the best-crafted characters in Transformers history.
In an earlier episode, when Starscream overhears a conversation between Thrust and Megatron about how they plan to keep him just to humiliate him some more, he proceeds to beat down every Decepticon in the base with the Star Saber. And succeeds.
Galvatron letting Thrust get crushed by Unicron. He'd actually started to deserve that.
For anyone else, jabbing Megatron in the foot with a taser would be lame. When the overweight and usually wimpy Fred does it, it's badass.
Punctuated by establishing one of his redeeming qualities: he's one of the few characters that shows actual sympathy for the Decepticons' Minicons. (Maybe because he relates to them, being pushed around by Billy and all.) He may not have converted Leader-1, but that hesitation was all Hotshot needed.
The comic book has a duel between G1 Galvatron (in this continuity a herald of Unicron) and Armada Megatron. It is very badass.