The hardest boss I've ever fought is the Egg Dragon from Lufia II. The battle is only about 30 mins long but you need to keep your team fully healed at all times because he can potentially wipe out your entire team in one attack.
The hardest enemy I've ever come across is the Gold Dragon, also from Lufia II. These guys appear in pairs at the bottom of the Ancient Dungeon which is a 99 floor dungeon which only has stairs that go down. The only ways to get out of the dungeon is to use an item that appears around the 20th floor, beat the dungeon or to die in which case all your progress is lost. The Ancient Cave is a randomly generated cave that is the only place in the game where you can find the strongest items in the game . There's also no save points in the cave so the entire cave must be done in one sitting and due to the nature of the cave it takes about 8-12 hours to get to b99.
With that explained I can get onto the Gold Dragon. They appear from around b90 to b99 and always come in twos. If you run into them it is instant game over unless you are insanely lucky. It's impossible to be faster than them and they are capable of wiping out a team of 4 99lvl chars with the best equips in the game before you even get a chance to attack or to even try to run. And then there's the whole thing of the 8-12 hours you've just wasted when you lose.
If anyone here has taken on and beaten a gold dragon I'd be incredibly fucking impressed.