The twilight itself seemed to put everything into a pseudo-stasis, basically taking a freeze-frame of a region, then allowing for movement. Therefore, water becomes ice, wind stops (allowing a certain valley to fill with poison), and people become nearly immobile spirits who move, if they move at all, in slow, mechanical, "pre-programmed" movements, like the regiments of soldiers moving in lockstep through Twilit Castle Town. Looking back on this, it appears to be a deconstruction of Going Through the Motions as well.
The final boss's death scene. It's a pretty common point of confusion the way Ganondorf seems to lose the Triforce of Power. At some point, long after viewing the scene for the first time, this troper realized that he's not losing it; the crest fading out signifies that it can't save him from being impaled by the Master Sword like it saved him when he was impaled by the Sages. Master Sword trumps Triforce-granted powers. Confirmed by A Link To The Past, where it's stated the sword was originally created with the ability to block the Triforce's power. A fragment compared to the complete Triforce is easily depowered.
Each stage of the final boss tests Link in a different way: for example Beast Ganon tests his beast form against your beast form, Horseback Ganon tests him on horseback with you on Epona, Spirit Ganon tests Midna's spirit form against his and Ganondorf is a final test of your skill as a swordsman. To me, Possessed Zelda is a test against you as a player, as you must use most of your skills to defeat that which you have sworn to protect. The analogy (that Possessed Zelda is a test for the player himself) makes even more sense when you consider this: You are essentially "possessing" Link, as a counterpart to Ganondorf possessing Zelda.
Ganondorf's silly reaction to the Fishing Pole: He's from the desert. He has no idea what that thing you're holding is. Of course he's going to keep his eyes on it, especially when you're bringing it out in the middle of battle with him! For all he knows, that Fishing Pole is some kind of Ultimate Weapon!
About the Howling Stone melodies, they each share emotional significance to the Link of Ocarina of Time.
The first is "Song of Healing", the song Link used in Majora's Mask to heal Mikau, Darmani, Pamela's father, and other suffering people.
Next is "Requiem of Spirit", which was the warp song for the final temple in Ocarina of Time, the Spirit Temple. Here Link had to travel through time and use both his child and adult selves to advance.
After that is "Prelude of Light", the first warp song learned and last one used to meet Zelda at the Temple of Time.
Then "Goron's Lullaby", used to soothe the crying Goron child in Majora's Mask.
"Ballad of Gales" appears odd considering the confirmed timeline, but is shares much of its melody with the final part of "Minuet of Forest", the warp song of the first adult dungeon, the Forest Temple, and a connection to Link's childhood friend, Saria.
Finally the "Twilight Princess Theme", the theme of Link from Twilight Princess, protege of the Hero's Shade. This was probably chosen to represent the new Link's rise to heroism.
This also makes sense, as the wolf seems to be a representation of the Stalfos that teaches Link techniques, which is implied to be the Hero Of Time.
It's often wondered why Zant's men took the children of Ordon Village away and kept them hostage, as they do not do that to anybody else in Hyrule. It's possible that Oo T/MM Link settled down in Ordon Village (where his descendant, TP Link, lives) and that Ganondorf somehow knew this, so it was suspected that one of the children might have inherited the Triforce of Courage. This could explain why TP Link was taken to Hyrule Castle instead of staying with the other children (as his... unusual reaction to the Twilight pretty much gave himself away).
Zant and light:
When Zant manages to attack you at Lanayru's spring and when he assaults Hyrule Castle, he (albeit temporarily) is in the Light. But he's a native Twili, and if going by Midna's reaction to being exposed to Lanayru's light and the fact she remains a shadow until Zelda grants her the ability to dwell in the Light he should probably be in pain, or not even there at least. The thing is like when Zelda gave Midna her soul/Triforce piece/whatever she did, Zant had received Ganondorf's ability to live in the Light, and thus was able to be in the realm of Light without harm.
Alternatively, he is the only Twili we see wearing clothes until the end when Midna shows her true form. Perhaps clothes protect them. And looking at Midna, perhaps not everything needs to be covered, but Zant's covered from head to toe.
Remember that fancy store Malo took over in Castle Town? Remember how the doorman wouldn't let you in unless your shoes were clean? Anyone who wanted to go into the shop had to go get their shoes shined by a little boy sitting near the steps for ten rupees. Malo Mart doesn't have the same restriction, meaning nobody ever actually needs to go get their shoes shined, meaning that boy has probably lost the vast majority of his one small source of revenue.
It's a little kid with a little pocket change hobby, he probably doesn't need the money to live. Also, with how much Link has done for everyone, it's possible that, off-screen, Link asked around for a job/family for him. Or there's another Malo Mart we never see because both cannons and teleportation are things, and the kid works there. Or he can move to Ordon Village, with fresh water, fish, and pumpkins aplenty.