Twinrova from Ocarina of Time is a memorable boss fight in the series, thanks to its climactic and theatrical aspect.
Majora's Mask's Goht is an excellent choice for top boss since its unorthodox racing and beat mechanics are a welcome contrast from other Zelda bosses.
Almost every Zelda game has some sort of dungeon, and the final challenge before completion is a final formidable adversary Link must defeat.
So, which boss is the finest in each 3D Zelda game? Link's first step into 3D is considered a classic for a reason