This is based on opinion. Please don't list it on a work's trope example list.
Nightmarefuel / Transformers: Fall of Cybertron
The Insecticon hives. They're, of course, swarming with Insecticons that come from every direction to attack Autobots and Decepticons, and the whole organic look just adds to the fear factor. Playing as Grimlock, you'll see these things come out of the ground and drag Decepticons down underneath it. To top it all off, you sometimes hear whispering-like voices coming from that sound like ghosts, which basically come down to seeing you as food.
Grimlock states that he was aware of what Shockwave did to him, implying he was conscious while he essentially had his body torn apart and rebuilt.
When Grimlock and Swoop go through Shockwave's lab, you'll see a few Insecticons that didn't survive the experiments. Fiddling with buttons can cause things like a saw cutting into one of them.
Sharpshot's death. Not that he didn't deserve it, what with the way he had helped brutally torture Grimlock, but still, playing through the way Grimlock literally tears him apart with his dino-mode's teeth is frighteningly brutal. Especially since Grimlock is supposed to be one of the good guys.
The Sea of Rust. Perceptor's words say it all:
Perceptor: Never have I observed such a traumatizing sight. An entire city of rust. Everything down to the last bolt is encrusted. Severe oxidation, pitting the metal's surface, gradually deforming its shape. I fear for the health of all Autobots. The supply of Energon may be on every Cybertronian's mind. But I have observed the encroaching and effects of rust on many Autobots. We must be ever vigilant to its presence, or this city will overtake us all.
For those of you who need more, an explanation; the Sea of Rust was once an ancient Cybertronian city from millions of years ago, so long ago that even the Autobots no longer remember who lived there. They were a peaceful and noble people, who prided themselves on exploring the universe — the Autobots and Decepticons discovered Earth from maps in one of their tomb-complexes. But something happened that destroyed the city, perhaps a war with some alien race, perhaps the accidental overload of some alien technology. What it was, the end result was the reduction of the city to a mass of ruins dissolving into so many flakes of rust they form a dust-ocean. Nothing lives there, not anymore. Nothing can live there, not even Cybertronians. It's just one huge barren spot — one that could potentially reach out and swallow the entirety of Cybertron. With the Core shut down, thus deactivating whatever automated defenses are in place against that fate... well, it doesn't paint a bright picture of the future.
The Riot Cannon for your enemies. Anyone hit with one single shot will be BLOWN APART. Arms, legs, torso and head go absolutely everywhere. It just shows how terrifyingly brutal Cybertronian weaponry can be, particularly when compared to ours. Needless to say, this is probably why it is Megatron's weapon of choice.
Megatron himself. We know he's an arrogant, vicious tyrant, but this game really sells home just how insanely deluded and full of himself he is. He outright refuses to accept his own hand is to blame for Cybertron's ruined state, going as far as to blame Optimus Prime, and he's so obsessed with being in charge that he's willing to destroy his own species outright if he cannot get his way.
The second and third stages make this very clear. In the second, he says he wants the Ark's energon supply, but at the end of the third, he wants to destroy the Ark. Even in the last stage, he sends Bruticus to destroy the Ark's engines, instead of sending the Combaticons to take the bridge. As the later stages data logs reveal, he knew what Shockwave was doing in the Sea of Rust and at the worst, just take the energon supply like Starscream did. There was no tactical advantage in fighting the Autobots, just let them leave and continue the plan in peace, since it's a winning strategy. Megatron ruined his own chance at victory because he couldn't stand the thought of the Autobots being alive and not under his dogmatic rule.