Evil!Maria is a sterling example of this. Her movements, her expressions, everything about her scream so horribly that this is something that looks human but isn't.
Her death scene is especially creepy. She laughs maniacally for several minutes as she is burned alive, all the while twisting around in a non-human, demonic fashion.
One of the few additional special effects from the Moroder version which truly improved the movie was giving the False Maria Glowing Mechanical Eyes when she opens them for the first time. It really helps to make the scene creepier.
The Moloch Machine sequence and the bit before, as the worker desperately tries to stop the machine going off, seeing the level rising. Then Freder seeing the machine turn into a shrine to Moloch, who consumes a horde of slaves and a procession of black-robed workers. It doesn't help that the Moloch scene has some unintentional Holocaust imagery, with workers being killed by gas and then led into what looks like an enormous oven... And perhaps the most unsettling part is that while the slaves have to be dragged kicking and screaming into the mouth of Moloch, the workers willingly walk into his jaws.
Freder's nightmare of the statues of the Seven Deadly Sins coming to life at the command of the Grim Reaper playing a bone flute, which then advances on him swinging its scythe.
