Alice. She is a Decepticon in disguise sent to kill Sam. She looks and acts just like a normal human girl so you would have no idea who she really is until it's too late. Her appearance doesn't help... Also, LOOK AT HER FREAKING TONGUE!
On the subject of Alice, what the hell was she going to do to Sam when she went on top of him in Leo's dorm room? Was she going to force him into having sex with her and kill him during it, or just kill him?
Just the fact that there are Transformers out there than can transform into humans are terrifying if they're Decepticons. Just the thought that not only could vehicles be machines, but humans as well.
The Decepticons besieging Earth and the Fallen's broadcast. For all the movie's faults, this sequence alone makes the Decepticons terrifying. Especially the brief moment where a 'Con grunt kidnaps Sam's parents.
The Fallen: "Citizens of the human hive, your leaders have withheld the truth. You are not alone in the universe. We have lived among you, hidden, but no more. As you've seen, we destroy your cities at will, unless you turn over this boy. If you resist we will destroy the world as we know it."
There's a brief scene when Scalpel and a team of Decepticons are going to revive Megatron from his watery slumber but in order to do so, they need to repair his missing parts. So what do they do? They proceed to tear one of their teammates apart just so Scalpel can fix Megatron. While the Decepticon does seem to survive the attack since the submarine sonar does pick up 6 "hostiles" instead of just 5 like there would be if the Decepticon had been killed, the way they just tear him apart and his muffled screams of pain and terror...
Devastator. Not only is he truly, horrifyingly enormous even for Cybertronian standards, but he's nowhere near humanoid — with a misshapen and hunched over simian-like structure — and it's outright stated that the Constructicons just being in the form is extremely painful for them both physically and mentally. And need we mention that he also has a miniaturised black hole inside his head that consumes everything in his path?
In an easy-to-miss shot: When the Fallen arrives in Egypt, knocking everyone to the ground with the shock-wave from his teleportation, he swings his staff and decapitates a soldier.
When Sam and Mikaela are hiding from the Decepticons in a hut, the sound of Starscream and other Decepticons roaming around and destroying other buildings rock the hut.
The look on Mikaela's face says it all. Her eyebrows are creased with fear, and she's covering her mouth with her hands, trying not to scream.