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.
Additionally, Din, who the Sages implied may have handed Ganondorf her Triforce piece as a prank (possibly even knowing what he did with it in the Adult Timeline), may have decided that her 'divine prank' had run its course, given her chosen champion had been defeated, and revoked her favor, taking the Triforce of Power away from him and leaving him to die.
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 it 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 OoT/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 even 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 any time 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 Move is called the Ending Blow because it 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.
Ganon's Sword is the sword used at his own execution. It created this white scar on him that was his fatal weakness. Canonically, the events of Ocarina of Time never happen in this timeline. No wonder he took the sword. It was likely the only weapon to ever seriously harm him.
The scene of Zant snapping his neck right before Ganondorf dies seems to be confusing on first glance, to the point that even the director didn't know about its significance. But Zant himself explains before his boss fight that when Ganon housed his power in Zant to recover, "[Zant's] desires will become MY desires". So when what's left of Zant, seeing his God's power fade and him on the brink of death, snaps his neck, he expresses his desire for Ganondorf to die. Which, despite wanting to the contrary, Ganondorf does by succumbing to the Master Sword.
Many players may find it a little odd that most characters react to Wolf Link in such an extreme way, and don't even seem to know what he is. Even the residents of Ordon think he's another monster instead of some canine, even though you'd think they'd have they fair share of dealings with wolves, since they're a rural community that raises livestock on the edge of the forest. Well, as it turns out, there are no wolves left in Japan, as all native varieties went extinct. Given that the game is made in Japan, it actually makes a bit of sense that most of the people in Hyrule have never seen a wolf before, nor know what to do when they see one.
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 it's 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.
With the nightmare fuel involved in Arbiter's Grounds in mind, let's think long and hard about what it actually is. It's a PRISON. A prison where the Twili were detained before their banishment to the twilight. Think about the contents of that prison. All the redeads and ghost rats and poes, and that's the stuff that must have moved in. The skull of Stallord is ancient. Very much so. So ancient, it probably was already there, maybe even alive. And the Death Sword. That is bound in a prison. Perhaps it was some kind of guard gone wrong? And all of the chains and spikes and bones. And gears. And quicksand. And advanced machines with death causing devices on them. You get the picture. Arbiter's Grounds was a concentration camp that culminated in banishment to another world not meant for humans.
This was likely a symbolic execution. Disagree? Let's consider that they sent Ganondorf through it to get rid of him when other attempts failed. The execution itself did seem rather ritualistic. For all we know, the twilight was just the final part of it, and they decided to just send him through. It's almost worse if it wasn't meant for execution. The sages willingly sent Ganondorf into a world that might have been filled with innocent people completely unprepared for a threat of that magnitude, as they had no Triforce to match his.
In the fight against Ganon, his weak spot is the scar left by his failed execution. One might assume that this means if you're a wielder of the Triforce of Power, you don't die and your usually lethal wound becomes a rather sensitive scar instead. Now, imagine if Ganon hadn't died (e.g. because he was attacked with a normal sword instead of the Master Sword) due to this protection. After enough fights, he'd end up covered in very sensitive skin that might just hurt whenever anything touches it. Meaning he'd be in constant pain. There's no known way to just get rid of a Triforce piece, is there...?