Boss: Without a doubt Ancient Automaton Koloktos. Really fun and not too easy boss fight, smashing him with his own sword was awesome aswell. One of my favorite bosses in any Zelda game
Mini Boss: Not to many to pick from here unfortunatly, but I'll have to say Scervo just because it was a new and unique fight.
Place: FunFun Island. Im very good at hitting the 50 rupee spot so it was basically endless money for me there, it was a very fun minigame aswell I think.
Dungeon: Lanayru Mining Facility for sure. One of the reasons I like Skyward Sword as much as I do, it had a really cool dungeon item and alot of puzzles that werent super easy. The only sad thing about it was the boss fight but whatever
Music: Ballad of the Goddess.
Moment: Just as Link flies through the air to finish Demise and The Master Sword gets hit by the lightning.