Easily, my favorite boss is split inbetween two games.
Baal, from Diablo II. The satisfaction of choosing a Necromancer, one of the most regarded "difficult" classes to be, and defeating Baal was worth every minute.
Ultimacia from FFVIII. The random party setup choosing three of my best characters made it even more satisfying when I made it through all four of her forms, and finally defeated her. The ending video made it all worthwhile.
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