Buffy was definitely afraid of Glory because every time they'd fight Glory nearly kills her! Buffy was also afraid of The Master, Angelus, Adam, evil Willow and The First.

Angelus and Willow both hurt her more emotionally, but I think Glory was the one who frightened her the most, for 2 reasons. Firstly because, as the above comment points out, Glory kept beating her each time they fought. Secondly because Glory was threatening Dawn. I think the fear of losing her sister was worse than the fear she felt when she learned the prophecy in season 1.

Even though Glory is probably my least favorite big bad the threat to dawn shook Buffy more than the threats to herself.