Scariest FF moment

I would probably have to go with Cleyra's destruction from FF9. The emotion wasn't even necessarily all fear, but it was still a very intense moment. The town wasn't just attacked, but utterly destroyed, and I was worried at first that none of the inhabitants escaped at all (though the PC's were obviously going to be fine no matter what). It's significantly different then the fear that you mentioned, but still quite scary in its own way.