i think that kefka, or sephy get coolest boss, but that's not this topic, so i think the hardest boss would have to be the ultimate slime thingy at the end of that long assed dungeon. if i remember correctly, you have to kill him in like 3 or so turns, or he runs away or sumthin lame like that. next would have to be the ultimate dragon from the same game. the one u fight if you collect its eggs or sumthin like that. with 65,565 hp, he has like the largest amount of hp a character can possibly have in an snes game. i spent hours devising strategies to kill him, so i wouldn't have to check the internet. turns out that after many frustratingly hours of devising, i came up with the same strategy as the one i compared it to online. so meh.
on a different topic, the most annoying boss is definetly gotta be doom gaze from FFVI. >_< you have to fly around until you get in a fight with him, and he runs away like a pansy after like 10000 dmg. forcing yet another 5-10 minutes of random flying to find him! >_<