Helmaroc King was greaat. Most of my favourites are from Twilight princess.
Stallord
This guy was awesome. Not the one from Link's Crossbow training duh, the one from Twilight Princess. I've always been a fan of the Spinner item in TP. Then having to use that as a medium of transportation and a weapon was so awesome.
Argorok
Argorok from TP was also really great. I'm pretty sure the hookshot is like, everyone's favorite item ever since they played ALttP or OoT. Then in TP when I first got the clawshots, I was like wow this new design looks awesome. When I played City in the Sky and got the double clawshots, it's like my dream came true. And i was really looking forward to the final boss and BOOM! Super epic battle with the dragon flying all over the place, especially the second phase when lightning was everywhere. The atmosphere <3
Demise
Well I love lightning, and this battle basically revolved around it. I always like forward to a 1 on 1 sword battle at an empty place as a final boss. Then when i got to battle demise this way I really like it. It was waay too epic, the music was awesome. It was so cool how Fi couldn't follow too. Then your skyward strikes don't work anymore so you gotta point it up and just get the power from the lightning instead. And the final blow was WAAY too epic. I will never forget that moment when I delivered the final blow to demise.
Yuga/Yuganon
The final boss for ALBW was amazing. I mean at first it really reminded me of ALttP Ganon, with the flying trident and such and I was thinking meh can't nintendo think of something creative? Then came the Bow of Light! I really wish this item was available throughout the whole game. It was soo cool how you had to merge to the wall and use the bow to shoot Yuganon. The most epic thing ever is when you gotta turn the other way around and shoot an arrow facing th opposite way so it travels throughout like the whole room. GOD this battle was amazing.
Vaati
Vaati from Minish Cap was a fun boss. I liked the final spider ish form. When you had to like make four copies of yourself according to which eyes were open. That was pretty epic
Onox
The first battle with general onox was not too bad, it was pretty standard. Then he turned into that dragon, now THAT was awesome. I love big bosses, and i love big dragons. It was cool how you had to jump on his hands to attack him and all, it was all about timing.
Twinrova
Duh, who wouldn't include them in the list. Well I loved the battle basically cus you gotta use their magic against them, like throughout the whole battle. When I first played OoT though i was thinking, when i just got the mirror shield, how would the battle be like. Would it just be reflecting light to the boss or something? And BOOM! I was blown at how you gotta absorb their fire and ice attacks.
Goht
Goht was such a fun boss. Just turning into a goron ball and spinning all over the place and ramming into goht was really fun for me. Then when the stalactites were falling from the ceiling, another awesome atmosphere created!
Twinmold
I love dragons, as i have said before. And i also love turning into a giant haha
I think there are more.. but I can't seem to remember right now haha