The current ones that gave me a hard time that  can think of is Satan and Lord DeRosso from Bravely Default. It was so frustrating when I would be doing so well when they suddenly kill me in a single turn... >: (

Dude, SNK final bosses in their fighters were stupidly hard. They were the main issues of those games. Too dang hard! >: ( Rugal I hated so much...

I was sleep-frakked during the last leg of Resident Evil: Code Veronica X, so I kept backtracking when I didn't have to, used up most of my ammo and fought the final boss using only a knife.

NEVER AGAIN.

Which is absolute bullshit, but it seems nobody in the world points out that flaw, but anyway.

@OP: recently I had trouble with Meta Ridley in Metroid Prime, but he's more annoying than hard. Then there was the Joker in Batman NES, which is more unfair than anything. Majora's Mask first form was also annoying without knowing what to do. But that's recently. In the history of ever, I don't know...

That seven forms guy from Gunstar Heroes can be hard as fuck depending on which forms he chooses. Cloud of Darkness in FF3 is hard because of bullshit. The final boss of MG Rising is also pretty tough (plus, it's ridiculously over the top, oh my god). And I remember having the hardest fucking time with Yunalesca (FFX) and Sigma (MMX4). And Sephiroth in KH2, Jesus. But granted, that's a superboss.

Yellow Devil from the first Mega Man is supposed to be hard, but I shamelessly used the pause trick.

Yiazmat from Final Fantasy XII, though not an overly difficult boss, was a painful experience that caused me to rethink my life. It took me literally three years of on-off playing to beat it, and I got nothing as a reward.

Every boss from the rebooted Ninja Gaiden series was a pain in the arse.

???

I don't think I ever used the boomerang on any of his forms. In fact, I don't think I ever really used the boomerang, period.

Anyways, I always hated Velius from Final Fantasy Tactics. If you didn't prepare for his fight, that bastard was a complete...er, bastard.

As I said, I don't really recall properly. I do remember throwing everything I had at him and only the boomerang working. You do need Lens of Truth to figure out final dungeon's pattern, though

That part's definitely true. I forget, can you actually enter the final dungeon without the Lens?

You can, with blind luck. It doesn't take that many tries, so if you do some maths you can come up with the result. But it certainly helps much more knowing the actual path you have to take xD

Krauser (Resident Evil 4) * My guns were pretty weak when I got to him.

and Carnage (Spider Man: Maximum Carnage) * This whole game is a nightmare.