For most retries, the Emerald Weapon in Final Fantasy 7. Time limit, regenerating limbs, powerful all-hitting counters whenever he is hit, an attack that drains one target's MP to 0 (so no Final Attack-Phoenix combination for you), an attack that requires you to use a limited supply of Materia, and more HP than any other boss. Even at Level 99 with multiple Master Materia this guy had me climbing the walls.
For most recent frustration, Beelzebub from Shin Megami Tensei 4. Yes, he is an optional boss in a legendarily difficult series with lots of insane bosses. From what I hear his earlier appearances have been just as brutal if not worse, but hear me out.
In this case, he shares an aggravating quality with a few other optional enemies in that he can spam Megidoloan, the most powerful Almighty (read: cannot be blocked, reflected or absorbed by anything ever) attack in the game. It inflicts about 500 damage to everyone, and a max-leveled party will have about 1000 HP on average, your main character probably a bit more. Regardless, he gets three turns per round. If he uses Megidoloan twice in the same round he will probably kill your demons. If he uses it three times, he is guaranteed to wipe out your party. He will always do this if you use the spell that has been your greatest asset for most of the game, the physical-blocking Tetrakarn. Nothing like a game that makes you bank on your opponent's mercy to survive.
He will still use Megidoloan on occasion in conjunction with his other attacks. These include an all-hitting projectile nearly as powerful with a high chance to crit and give him a fourth or fifth turn, but that can be managed if you bring demons which resist or negate it. The real killer outside Megidoloan is Pandemic Bomb inflicting Sickness, the most broken status ailment in the game on your entire party... because 9 times out of 10 he will immediately follow it up with Death's Door reducing the HP of everyone with that ailment to 1. If he does Pandemic Bomb, Death's Door, Megidoloan you are once again screwed. It's actually a relief when he uses all-hitting Instant Death spells or stat-reduction because at least those can be blocked or undone.
But wait! There's more! He always gets the first turn when you fight him. He has the highest evasion in the game. Even Megidoloan can miss him, something I'd never seen happen before then. When you miss, your target immediately gets to take their turn. He has no elemental weaknesses and high physical and magical defence. You have a multitude of effective stat-reducing moves you can use on him, but if he's affected by three or more of these he will dispel them, same as if you put too many stat-enhancing moves on your party. Finally, when he's down to half his health he starts spamming triple Megidoloan regardless of what you do- the only way to survive is to reduce his attack power and increase your defence to the point that it only does 300ish per cast... something that won't last long. Finally, before fighting him you must beat a weaker pre-boss who uses Pandemic Bomb as well, only serving to weaken you before the real thing.
I've beaten a lot of hard RPG bosses in my time, but none caused me as much trouble as those two jerks.