MagiMaster wiped me out once, but at the time I didn't know about the benefits of casting 'Beserk' on him. The Three Goddesses were somewhat challenging, but not particularly so. First couple of times I tried to defeat Kefka I also failed.
Atma Weapon was a walkover - first time I played through, I just 'Rasp'ed him into oblivion; on subsequent occasions, Vanish + Doom did the business. Some people say it's cheating, yet strangely I care not.