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 and the Hero of Time Passing the Torch to him as the Hero's Shade.
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.
Midna being only partially clothed may also be justified by the fact that, when at full power, she wouldn't need to wear any kind of protective armor as she could simply cast a protective spell of sorts.
The Hylian soldiers in Twilight Princess have an uncharacteristic level of cowardice compared to other Zelda titles. They're easily scared of Wolf Link whenever he's in town, and when a group of them volunteered to escort the civilians to Kakariko village, they ran away the moment Telma mentions that the path would be filled with monsters. But considering what had happened to them up until now, it's not all that surprising:
Zant's attack on Hyrule castle no doubt killed several soldiers without them barely being able to fight back. With Zelda surrendering to Zant added into the mix, morale would suffer a devastating blow and not likely to recover anytime soon.
With several soldiers now dead, new men, who would otherwise be unsuited for a military career, would most likely have to be drafted just to try and keep any semblance to Hyrule's military might.
Among the golden bugs you can find there are two snails. If you check their descriptions, it seems Link is not sure which one is the male and which is the female. In real life, most snails are hermaphrodites.
The Finishing Blow is called the Ending Blow because it is the one that is the one that, in a sense, ends the game by finishing off Ganondorf.
The Gorons in Castle Town charge moderately more for their items than most other shops. The young one on the ground floor says his dad calls it "regional pricing". Makes sense, as the only other shop in the area charges thousands of Rupees for its goods, and most potential customers don't teleport. (Of course, then they may end up being a casualty of Malo's buyout, as now they have the highest prices anywhere...)
Most dungeon bosses have an eye (which may not belong where it is) that both functions as a weak point and turns into a Heart Container upon the boss's defeat. This may be a Japanese pun: eye = ai (love). Which comes full circle when you beat Blizzeta and the Heart Container comes from an expression of ai.
When ascending the tower of Hyrule Castle to confront Ganondorf, transforming into Wolf Link allows one to see the ghosts of dead soldiers at a certain point. These soldiers probably died defending the castle from Ganondorf, and guide the way in hopes of being avenged.
After playing through Skyward Sword, the City in the Sky takes on an entirely new perspective. One can only assume its what is left of Skyloft after all these years. The place looks positively futuristic compared to olden times, but in the end, the place is falling apart, and not just because of Argorok. It's really kind of sad in that way.