I'm glad Yiazmat from Final Fantasy 12 got a few mentions, it's the only FF super boss I've ever given up on. Whoever decided that he should have the Death status attached to his regular melee attacks needs a good slap in the face. SO monotonous having to constantly revive and reapply buffs.
On the other end of the spectrum, I really like the boss fights in FF 6. They don't have much health, but they can still dish out an ass whooping. It makes the fights really intense and they don't overstay their welcome.