Yeeeeaaaaah, for me... the coachman from Pinocchio, although intentionally scary, when he made this face [link] he scared the hell outta me beyond aaaaany expectations I've had, and I was already sufficiently creeped out by the puppeteer
It seems like a lot of people are mentioning intentionally scary characters.... Anyway, not technically a cartoon, but a puppet... thing. On Allegra's Window ... Well all the puppets are actually pretty creepy, but that cat and dog are horrifying.
"Night Of The Wheremole", blond violin girl and that puddle woman from Courage The Cowardly Dog; Higurashi no naku koro ni (full of scary scenes) and probably Paranormal Activity (I only watched part 1).