FFT: Wiegraf. I remember the first time I played through it FFT seemed almost impossibly hard, though with age and experience I now have limited trouble with most of the game. That being said, Wiegraf is never easy.

Suikoden II: Luca Blight. This may be more of a "Wake Up Call Boss" according to that article (except you're not supposed to learn much from it; it's just surprising), but boy he was tough my first time through. Although I actually thought you had to defeat him with all three parties... yeah, shut up.