Captain Stalfos: Har-Har-Har-HARRR!!! The human! You carried out all the tasks my useless crew set you... Then you saved this Hideaway from our most deadly enemy! Truly, you're made of the right stuff to be a pirate! But there's one problem... You've got too much flesh on your bones! Skull and bones! That's the pirate symbol! So, human, let's begin the ceremony... We'll soon get rid of that meat of yours! Become a skeleton! Become like us! Your screams as I strip the flesh from your bones will mark your birth as a pirate! As one of us!
Junglo's pet Mandrill seriously doesn't like Tingle. Especially when you use her as a bridge, and you are gonna have to do that a couple of times.
The ghost girl's story by the end of the quest to help the Guard/cure the Guard's wife.
The song playing in the Deku Tree, which is a version of Saria's Song from Ocarina of Time played as if it's merely an echo from long ago times.
The death of the Deku Tree. Allthough it is averted in that he momentarily stops dying because he forgot to reward Tingle for his help. Also, the Deku Sprout being all bold on fullfilling his role as the new Deku Tree, but not knowing what actually he is supposed to do because the former Deku Tree never told him, is not helping the drama.
The end of the map quest, when the old lady is revealed to have either died while you were away or have been dead when you first met her. Her ghost's purpose in the land of the living was her late husband's wish for them to run a successful map shop, so when that's done, she goes with a smile.
The story of Baron.
That One Level: Insect Cavern. You can't see a thing. Even if you come across one of the few places you can buy a firefly's services and hope to pay enough to be lighted your time in the dungeon, it's hardly an upgrade. It's also one of the largest dungeons in the game and has some very tough enemies.