This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Cloud Atlas
The hallucination sequences with Zachry and Old Georgie hisself. Imagine the The Devil mixed with a particularly evil looking Witch Doctor and voice that can make the ground shake. Georgie even serves as Nightmare Fuel for Zachry as well, as he always gets a Oh Crap! look on his face every time he rears his ugly mug.
The Fabricant slaughterhouse.
The cafe where Sonmi~451 works feels a bit too clean and inviting in that Uncanny Valley kind of way.
Interestingly though, the pristine cleanliness of the diner (when open), contrasts strongly with the reality underneath the digital and holographic veneer, Papa Song's, is actually quite shabby. Perhaps the idea that was meant to convey is that the glossy corporate image is all fake and superficial. Artificial people (the fabricants) as workers, a fake veneer, and quite possible, fake food as well.
The Kona Tribe is basically walking nightmare fuel, with their creepy makeup, how fast they show up and the fact that they are cannibals.