Undertale/Nightmare Fuel

For such a whimsical game there is a lot of creepy elements.

• Everything related to Flowey, from his personality, to his laugh, to his ability to change faces (at some point, he morphs showing the faces of every main character, including the player), to the reveal of how such a deranged being came into existence.
• The True Lab. An apparently abandoned laboratory/hospital with clues that experimentation in living beings were practiced in the site, a gloomy atmosphere, Eldritch Abominations roaming freely, and you can't escape the place.
• The ending of the Genocide route.
• The hints about the existence of W. D. Gaster, particularly if you played the version of the game that activated the random appearance of his followers after having played the version where you has to hack the game to have access to such events.
• Any moment where Sans shows his competent side. His Wham! Line in MTT Resort where he plainly says that, has he not be bound by The Promise he would have killed you (which remember, are a small child) strikes as particularly chilling.
  • Sans' "shortcuts" can be unnerving.