I'm going to include a certain selection of bosses from each game, mainly because I see no point in including obscure guardians like Digdogger or Horsehead.

My vote for best Zelda boss would have to go to Goht from Majora's Mask. I'm a huge fan of the final battle in Wind Waker, but it was a little too easy, which is why I voted for Goht instead.

Goht's battle was just amazing. It was one of the most genuinely entertaining boss fights I've ever encountered in a game up to this point. It took me a few minutes to figure out exactly what the hell I was supposed to do, but after it clicked, I was grinning throughout the entire fight. Challenging and inventive.