Luca Blight in Suikoden 2 is probably the single best one. You need an army, three parties, and a duel to kill him.

Brayko in Alpha Protocol is a son of a bitch in plot, a son of a bitch to fight, and is incredibly fun and satisfying.

Ornstein & Smough, holy trout if you weren't genuinely working on your skills as you play, smurfing :rip:.

Undyne in UnderTale.

Morrowind doesn't have many boss fights as such (though you can go attack characters as powerful as demigods, as well as actual gods, if you want.) but everything about the confrontation with Dagoth Ur is incredible.

And Gilgamesh in FFV, of course!