"Until that day...'till all are one." Those last four words would recur in numerous Transformers series, bordering on Arc Words for the whole mythos.
Optimus's death actually had kids walking out of theatres crying, refusing food and locking themselves in their rooms. Serious shit.
And the touching Vince Di Cola theme for the scene.
Many are likely to disagree, but it's Megatron's "death". Megatron has always seemed so strong and menacing, a Nightmare Fuel character to the hilt. To see him humbled so and then abandoned was expected for the den of evil that is the very definition of the Decepticons in the G1 cartoon. What is truly inspiring is that this powerful figure, reduced to such a pathetic state, has no choice but to plead for help. After which, without hesitation, Soundwave picks him up and carries him, saying, "As you command." Soundwave has never had a better moment.
Of course, not even he nor his other minions object to unceremoniously throwing him out with the other injured Decepticons. And done personally by Starscream to add insult to injury. Optimus died with dignity, cherished and surrounded by respecting comrades. Megatron "died" being ejected into the cold void of space by his troops like dead weight.
Actually, it's more the way Optimus Prime just calmly picks up his rifle as he's about to do the deed. One of the greatest rivalries in animation, about to be ended in a manner far more reminiscent of someone putting down a rabid dog (which a baby-killer like Megatron actually is, really). Though the way Prime blows off Megatron's pleas for mercy still make it a Moment Of Awesome.
Not to mention the music in that scene was AWESOME.
The scene preceding Optimus's fatal wounding — where he charges in and basically takes out half the Decepticons single-handedly — contains The Touch, Stan Bush's one contribution to popular music that has withstood the test of time. The sheer, barnstorming track combined with Optimus Prime's awesomeness just puts you on a hell of a tear-inducing high that gets smashed right back down when Optimus gets fatally wounded. And then the track comes back in the finale, when Rodimus Prime arises.
Seeing the Autobots getting slaughtered on the shuttle, with Ironhide begging for mercy before getting his head blown off.
Actually, rather than begging for mercy, that might have been something of a Moment Of Awesome for Ironhide, the Autobot in question. His friends have just been killed in front of him, he's barely holding on to life but then Megatron gives his grand villain monologue about how he's going to use the shuttle to destroy the Autobots on Earth. Ironhide then grabs Megatron's leg, giving a weak but defiant "No!", still trying to stop him and save his friends. Which makes Megatron's statement of "Such heroic nonsense", followed by casually killing Ironhide, even more chilling.
Prowl's horrific death, just before Prime's.
The final scene of the movie after Hot Rod becomes Rodimus Prime after touching the Matrix. After inadvertently causing Optimus's death, he fulfills his destiny and finally finds his redemption as Optimus says through the matrix: "ARISE, RODIMUS PRIME." Hot Rod can do nothing but whisper "Optimus." Then proceeds to unload a can of whoopass on Galvatron and destroy Unicron from the inside as well. Tears of awesomeness for sure, especially with the music track which was most appropriate.
The deleted scene where Ultra Magnus leads most of the characters who didn't show up in the movie (Sideswipe, Inferno, Red Alert etc.) to stop Devastator. They blow him up and force him to split into the individual Constructicons. The Autobots, being outnumbered and having used up their weapons flee, but Scavenger (the Constructicon who killed Prowl!) shoots Red Alert in the back. Inferno cries out to his best friend, but Ultra Magnus holds him back. Finally Inferno transforms and flees with the others.
Another storyboard shows that Megatron was laughing at Red Alert's demise. (That's what he was looking at when Optimus comes to fight him.) Anyway, the gun Megatron used to kill Prime was Red Alert's! There was a deleted shot that showed Red collapsed in front of Optimus and Megatron during the fight. You can tell that he dragged himself over there and dropped his gun when his spark gave out.