The station for KD’s Flight of Fear originally had clear tubes stuffed with dummies meant to look like the corpses of park guests. There were kids with stuffed animals, mothers with purses, etc. curled up in the fetal position and apparently embalmed inside the tubes. At some point they were replaced with the alien figurines you see today. KI’s FOF still has the original figures, but they’re wrapped up in tarps.
Revenge of the Mummy’s fake-out ending where the ride op literally gets devoured by Imhotep is pretty disturbing (and awesome) too.
Literally all of Alton Towers’ coasters. I think the smiler has one of the best themes for a ride of all time. I mean, for a time the rides slogan was “get corrected.” Does it get any creepier than that?