Megatron. Giant, genocidal lunatic made of jagged alien metal with a booming, snarling voice. Can't be stopped or slowed down by normal means. Ripped Jazz in half with his bare hands like it was nothing. CGI just a little too realistic, there... Megs looks entirely too much like they actually had a giant alien war machine in front of the camera.
Speaking of Megatron, the "I smell you, boy!" line that he said when chasing Sam up the abandoned warehouse was quite creepy.
Megatron's mutilated face in DOTM. Not to mention that he has several Scalpel-esque robots crawling around in his giant gash.
The death of Ironhide. Here's what happens. Right after the Highway Chase scene and the Mexican Standoff scene, Sentinel reveals his role as the Big Bad of the film and shoots Ironhide two-three times. You'd think that would be the end of it. But no, you witness Ironhide rusting up and dissolving to the point where his head falls off his shoulders and the rest of his body just sags apart. It's such an emotional punch and to hear Ironhide groaning and letting out his last breath is nightmare inducing.
It's also horrifying because it happens completely out of the blue. It is completely unexpected.
The Decepticon's apocalyptic takeover of Chicago. Complete with genocide and screaming survivors. And people getting vaporized onscreen! A skull fell after one person was shot.
Laserbeak, full stop. He could be anywhere, pretending to be anything, not to mention the fact that he's a merciless, coldblooded killer.During the film, Laserbeak takes on a series of insidious disguises, including a printer, a flat-screen television and a computer monitor. However, that quote comes from when he turns into a pink Bumbelbee-esque robot and befriends a little girl to kill her father.
"Is your daddy home?"
Shockwave's "pet", The Driller. Imagine a mechanical worm that's bigger than Devastator, with a mouth made of a series of buzzsaws and grinders, and able to dig and hide underground and unleash terrifying destruction.
It also becomes a bit of Fridge Horror when you learn that it's actually a domesticated Cybertronian beast (similar to Laserbeak, Ravage, and the Insecticons). Meaning that at one point there were hundreds of them burrowing through Cybertron.
Remember that car your girlfriend's boss gave her? That $300,000 car. It's a Decepticon, specifically Soundwave, and he's just kidnapped your girlfriend, threatening her with his tentacles.
Alice... Just 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!!!
In ROTF, the Decepticons besieging Earth and the Fallen's broadcast.
For all the movie's faults, this sequence alone made 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."
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. . .
There's a brief scene in ROTF 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. Granted, 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, but still... the way they were just tearing him apart and his muffled screams of pain and terror are just... *shudder*
"No prisoners... Only trophies..."
That blue energon in the first movie that's supposed to be Symbolic Blood...In ROTF and DOTM, it's been replaced with red energon. Seeing giant gobs of blood-colored energon flying at you whenever an Autobot or Decepticon got ripped apart...
"Laserbeak, kill them all."
Starscream's death. Just imagine all the pain he went through. First one eye is ripped out and then another has an explosive device stabbed into it. He spends his last seconds screaming while blind before having his head blown in two.
You wouldn't want to listen to the track "Cybertron" from the first movie alone in the dark. 0:51 is where the really chilling stuff starts.
"The Fallen", from the second film, is even worse. Synthesizers and vocals don't mix, kids.
From the original comics in the 80's comes the Smelting Pit. A place where Decepticons toss captured Autobots, and they melt and desolve to death slowly over several days. Made worse as we see Scrounge, a charecter we'd gotten to know in the previous issue reduced to a torso, then melt to nothingness, while his friend Blaster tried to save him.
From IDW's Spotlight mini-series comes the Kup issue. The story begins innocently enough with Kup fighting off zombie-like Cybertronians, before retreating to his rough hut/shelter. Initially it seems like he's merely surviving a rash of zombified Cybertronians alongside Outback after having crash-landed on a strange planet, but then the true horror element shines through: Kup has actually been driven insane by the radiation coming off the exotic variants of Energon Crystals glowing on the planet, and Outback is actually dead - Kup does not notice this fact as he brags to Outback's own corpse while using his arm as a crude club! The way the art style takes on a surreal, dreamlike approach when the narrative is in Kup's point of view makes it even creepier. The later parts of the story add a bit of a forlorn horror to it, as it turns out Springer was sending Autobots in hazard gear that made them look like zombies to the addled mind of Kup in an effort to rescue him, and in the end it takes Trailblazer's forcefield ability to get Kup out of that brown hellhole, at the cost of Kup nearly busting his Spark chamber's containment field in a fashion akin to a stress-induced cardiac arrest!
Another IDW-given form of Nightmare Fuel is the Cybertronian punishment of empurata. Those found guilty of heinous-enough crimes are modified extensively to remove most forms of their outward identity. Their hands replaced with unwieldy clamps or other job-appropriate appendages, their outer chassis swapped around quite a bit, and their face rendered a single, mostly unemotive optic. The questionably sane Autobot Whirl is one to have suffered this fate, and occasionally thinks back to a time he looked normal. The most prolific victim of this process, however, is a senator who prided himself on looking good, could scarecely keep a single paintjob, and was a good friend of Orion Pax. The one who gave the order did so soley out of spite after finding out he was helping Pax in his movement to change Cybertron's government. The result of this process? Shockwave.
Oh, and that spoilered character above? He was also subjected to Shadowplay. A process that inverts the personality of the victim. Turning Shockwave from an emotional compasionate being to the coldly ruthless logical monster we all know now. They didn't just maim his body, they butchered his mind and soul.
There's a quick, but brutally creepy scene from the construction of the Kaon underground gladiator arenas in Megatron's origin story - several Constructicons are shown to obtain some of the raw material they need by melting down some of their enemies. Given that the prisoners were restrained, they were most likely still functional and concious before they were thrown into the smelting pit. Yikes.
In Arcee's Spotlight, the way Jhiaxus was depicted modifying Arcee to alter and give her the female gender is incredibly creepy. Arcee herself has some emotional stability issues as a result of what was done to her, and when she later got her revenge on Jhiaxus in a later comic, she kept attacking his helpless body ruthlessly even after severely crippling him, with a wicked Slasher Smile on her face as she got her revenge.