I would say Seymour's third form/encounter on top of Mt. Gagazet from Final Fantasy X.
Probably the first boss that actually stopped me cold in my tracks because I did not see him coming. Since this is his third time around, his stats are obviously raised and he is faster than any of your characters, so he often attacks first and is able to land two hits in a row. His main strategy consists of hitting one of your characters with his staff, inflicting the debuff called Zombie, causing the opposite effect of healing spells (i.e. instead of healing, you take damage). Since he can attack again, he promptly casts Full Life on your zombified character, causing a 1 Hit KO. He can also cast Flare (strong non-elemental magical attack), and can use Curaga on himself, and if you summon an Aeon, he can kill it with one hit.
What made this boss so hard that you did not see him coming and there was no way that you were prepared to take him on. There is nothing in the immediate area in terms of random encounters that would cause you the need for blocking the Zombie debuff. I literally grind for days just to get my characters stats up and to create some Zombie-proof armor. Even so, I needed to practice my strategy in order to beat him, and that also took a few days.