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Each Ganon(dorf) fight from Ocarina of Time, Wind Waker, and Twilight Princess were definitely awesome. Kudos to the big guy for never letting me down.

From OoT, Phantom Ganon and Bongo Bongo were great bosses. I mean, seeing Phantom Ganon come right out of a picture frame blew me away. And as for Bongo Bongo, fighting a giant specter on a giant bongo was pure sweetness. Oh N64 era graphics, how you spoiled me so.

In Wind Waker, Mogera and Gohma were great bosses, if only because of their sheer size and ability to intimidate.

In Twilight Princess, Stallord, Argorok, and Zant were all really memorable bosses. Stallord because of the great use of the Spinner, Argorok because of the great use of the Double Clawshot, and Zant because he's just plain awesome.