so many little things creep me out more or less. The Sacred grove in Twilight Princess, ReDeads (especially the way they scream) Bongo Bongo, to a lesser degree, the silent realms in Skyward Sword
also the Skull Kid in Twilight Princess, the way he giggles and calls the puppets out to get you. The Skull Kids in Ocarina of Time were kind of cute in a way, how they danced on the stumps while playing their flutes