I'll go with Emerald Weapon from FFVII (I didn't have the underwater materia, meaning the 20 minute time limit kept things interesting...) as the hardest boss I've ever fought. It took forever to get the items and leveling I needed for that...
Other bosses I liked a lot are the Bowser's from all the Mario games (1,3, Super Mario World and Super Mario 64, specifically). I thought they all required at least a decent amount of skill.
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