probably said a dozen times, but...
i would have to say the 2nd hardest was the weapon (forget name, omega?) on the last stage of ff8... he was a bitch and you didn't get crap, but it was worth it if you actually beat him.. sheer joy from beating such a bastard
hardest would be omni (right name? sphere boss) on ff9... sonuva, he was evil... beat him after the 5th try or so, geez.. it takes pure luck really