The possessed puppets in Vagrant Story are reasonably creepy - especially when you learn that one variety are inhabited by the souls of violent criminals, while the other kind are vengeful children who were killed in the earthquake that destroyed the city. Either way, they're pint-sized mannequins that lurch around clutching knives or daggers and squeaking playfully. Unsettling stuff.

FFVII's Jenova had some creepy forms, too. Especially Hojo's 'heretic' transformation, and the Birth/Life/Death phases.