I made an account just to post in this topic. The hardest boss I've heard of is but never fought is probably the Demi-Fiend from SMT games.
The hardest bosses I've fought but never beaten are the Life Keeper from Chocobo's Dungeon 2 (not technically a boss, but I've never been optimized well enough to kill him and he's given me literal nightmares), The Dark One from Arc the Lad II, the Death Egg Robot from Sonic 2, and the final Bowser from Super Mario 64.
The hardest boss I've fought but actually beaten is Zophar from Lunar 2, who took me 15 years and hundreds of failed attempts to beat. Once you get to his dungeon you can't go back and buy stuff; you're stuck.
His first form isn't so bad, but his final form scrunches your party members into an enclosed space so area attacks affect multiple members, he gets around 4-6 attacks per round via his separate hands, is insanely fast, and if you kill one of his hands or take awhile in fighting him, he gets angry and can do an attack which hits for over 7000 damage when your max HP is 999 (you can survive it with a 60-MP protection spell when your max MP is about 240 at level 57 for the fastest character), and you pretty much need to do that because one of his hands heals the others and his main body. One of his attacks hits the whole party, others can drain HP and MP, and he can also heal himself. All of his parts have a load of HP, and each hand has different weaknesses and abilities. Before you start the second form properly you have to fight the invulnerable first form, forcing you to waste turns defending or buffing. And both forms have unskippable, lengthy cutscenes in between them. When I finally beat him, the unloseable phase 3 took a while because I was completely out of magic, MP-healing items, and HP-healing items. By the end I just kept swinging until he finally, FINALLY fell. Apparently the Sega CD version of him was even worse.
Rahu from Custom Robo for Gamecube was also really difficult; when I won I had 2 HP left.
