Irenicus, in Baldur's Gate II, was the most difficult boss I had to fight (time stop, invulnerability, speed, time stop, wail of the banshee, death finger, time stop, wail of the banshee, another kill-you-all spell, time stop...)
I had to do the "I summon lots of monsters" and the "I am launching area of effect spells while actually not seeing you" tricks to be able to beat him.
Another one would be Omega in FFV (an optional boss), you had to use X-Fight and hope you will be able to kill it REAL FAST.
As for Shinryuu (the other optional boss), he was very easy if you used some water-protecting rings (tidal waves that heal you ? hmmm yummy)