Clownpiece from Touhou 15: Legacy of Lunatic Kingdom. When a Stage 5 boss on Normal is harder than that same game's final boss, Extra boss and most of the final and extra bosses of the rest of the series, you know something went wrong. This girl is complete and utter madness, both literally in-game and also as a game boss.

The Sleeping Table from Persona 3 FES, probably because I didn't have Mediarama. I literally could not have healed back all the damage it dealt if I dedicated all my turns to using healing spells, and two of its spells were enough to wipe out the entire party. I eventually had to resort to going all-out offensive and simply using the equivalent of Megalixirs to heal every time it used its powerful moves.

Chac from Final Fantasy X-2. You have a couple of ways you can abuse her AI to guarantee your win. And you damn well better use them because her damage output is far beyond your capabilities to endure, and a single mistake ends up with a character lost for all time. If you don't AI abuse you have to come up with very specific ways to deal with her every move. She's a superboss, but she's so far above and beyond anything in the game up to that point I felt the need to include her regardless.

I'll need to think about the other two for a bit longer.