Unicron. Not only do we get to watch him devour an entire planet within the first few minutes of the film, children and all, but later we even get a charming trip through his innards that includes shredding claws on tentacles and a giant bath of acid his victims are dumped in. The latter actually shown in action with victims struggling and flailing as they melt. Watch it here.
Unicron's theme is very effective for setting the mood. I bet I'm not the only one who finds it appropriate for The Borg.
The composer for the BGM of this movie, Vince DiCola was also working on Rocky IV at the time. Ivan Drago's and Unicron's themes have more than a passing similarity...
The Japanese version of this scene is even worse. Unlike the original, where Screamer is completely silent as he dies, there he screams in agony after he's shot, then his scream fades out as he goes offline.
Prowl being shot by Scavenger in cold blood would normally just qualify for Nightmare Fuel. But the fact that we go close-up on his eyes glowing red and smoke pouring out of his mouth before he collapses...
Ironhide's death may be just as bad. It's one thing for the Big Bad to start shattering Plot Armor like it's tissue paper, but shooting you point-blank in the face when you're already down on the ground, and cracking a joke about it? That's dark. Making it a Sound-Only Death really doesn't help, considering the scene cuts away to an external shot as we see the power buildup in Megatron's fusion cannon as it's about to fire, and especially since the song "Instruments of Destruction" comes to a definitive end immediately after the cannon discharge is heard.
Imagine this: You're a young child who has watched Transformers for years. Imagine the horror on their face when almost every character they grew to love is killed by Megatron on the big screen. To sell toys.
You'd think a world-gobbling planet is scary? Wait a fucking second, DID IT JUST TRANSFORM INTO A GOD!?!?! Yes, Galvatron, we feel how scared you are. Even worse is that, unlike the real God, Primus was DECIMATED by Unicron. That gives you an idea of his power and how utterly screwed we would've been if Rodimus Prime hadn't been able to open the Matrix.
The Japanese version of the movie, of all things, was very chilling. Especially the opening scene. Screams were added, making it more creepier than it already is.
It's worse when you see ships trying to escape only to get pulled back down with the planets they tried to escape.
What's even more scary is that this god can travel dimensions just so he can devour his brother, Primus. What do you think happened to the Go-Bots?