If there's one reason I play Zelda games, it's for the bosses. I don't love dungeons, but I put up with them because the boss battles that come after are, at the very least, fun - and quite often they constitute the absolute highlights of Zelda games. Which one was your favourite, from any of the Zelda games? I'm split between two. First would be Zant, from Twilight Princess. That fight is utterly epic, and manages to convey, like, the entirety of Zant's absolute craziness over the span of a single battle. Really cool. The other one is the final battle with Ganondorf in Wind Waker, which I think was the first case of Zelda being really useful when fighting a boss. Had an amazing atmosphere, and I just love sword duels in general. Not hard, but... epic.
I've always found the Spirit Temple from Ocarina of Time against the two witches very fun. It's not particularly difficult, but the whole sequence to damage that boss is very fun.
I'm going to go old school and choose Ganondorf. He's the only real boss I can honestly look back and remember well. The only one who seemed like a proper one to me anyway.
After replaing Twilight Princess, I have to say he was pretty good as well. I'm on my playthough of all the Zelda series so that might potentially change if there is another great boss out there! Zant was good.
My favorite boss is the final boss in skyward sword. I just like how I use lightening to charge my sword and then get a hit in.