I don't remember watching Courage the Cowardly Dog much as a kid, but King Ramseys was pretty disturbing. The way he says "Return the slab, or suffer my curse" is pretty freaky.
And speaking of freaky, Freaky Fred is just plain creepy. Especially when he began trimming Courage's fur. Fred's grin is just really unsettling.
The blue fetus thing didn't scare me that much. I found it more funny than creepy.