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. I don't think fire would go out if it was lit before twilight descended. - Landis
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.
I kind of interpreted this that Link had proven himself more powerful than Ganondorf in every way. Thus, the Triforce of Power switched allegiance.
That last part makes more sense when you think about the fact that 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 possesing Zelda.
Puzzling over Ganondorf's silly reaction to the Fishing Pole recently led me to a hilarious conclusion: 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.
The Hero Shade has been confirmed 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).
So, it's been confirmed that the Hero's Shade is a manifestation of Ocarina of Time/Majora's Mask Link's regrets of not being able to pass on his abilities and skill to those after. Now, for the most part this makes sense, as he was returned back in time to be a child and nobody had any memory of his adventure nor believed he was a hero. But then you wonder, why didn't that Link just pass on those abilities to his kid(s)? He must have HAD at least one child, as Twilight Princess Link is his descendant, and surely they could have taken after their father. With this in mind, we're left with three possibilities, in ascending order of sadness: 1. Link had a distant/cold relationship with his child. 2. He or she was somehow disabled (e.g, blindness) and unable to take on the abilities. 3. Link died before his child was old enough to learn.
Or, much more simply, his child wasn't or didn't have reason to become a swordfighter.
The possibility of Oo T Link having a child is 50/50. It's known that Link is reincarnated after so many years, each new Link being an entirely new incarnation (though with similar characteristics), and not necessarily being a blood-descendant of past heroes. Link's regrets, therefore, could be simply having no one at all to pass his skills and knowledge to.
That's already been Jossed by Hyrule Historia, which confirms Twilight Princess's Link is indeed the descendant (not reincarnation) of Ocarina/Majora's Link.
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.
Think about the Arbiter's Grounds for a moment. In a Gerudo Desert, has some stylistic resemblances to the Spirit Temple from Ocarina of Time, was used as an executioner's ground by the sages...and there are no Gerudo in the game save Ganondorf. There's a good chance that all those undead in the Grounds are the result of the Hylians "dealing with" the rest of the Gerudo.
Except Four Swords Adventures, which takes place after TP on the timeline, shows that the Gerudo are still around, and have relatively friendly relations with the Hylians.
It is established that using his wolf "senses" Link can see spirits (when in Twilight) and ghosts. Now think about when he's fighting his way through the castle and eventually he'll comes across some ghost soldiers who show him the right way... We know there where soldiers patrolling the castle still after Zant took over (we saw their terrified spirits in the twilight), so we can only assume they where all slaughtered after Link restored Light in the Lanayru province.
It also helps that a number of them can't be ignored: if you want to go certain places, you have to deal with them or they'll hit you and set you back (think the Piece of Heart in the Snowpeak Ruins lobby; you have to beat the Imp Poe or he'll keep you from getting to it); some are in the cave of Ordeals and counted as enemies, so they have to be defeated to get the door to open; four are even part of one dungeon's puzzle. Also, the reward for beating 20 is tied with Rare Chu Jelly for the best potion in the game. (The reward for killing 60 is a bunch of Rupees, so, meh, but if you want 'em, or just want to see what Jovani really looks like...)
At one point, Midna tells Link about how she heard legends of the Mirror of Twilight and how it could potentially lead them back to Zant. Question is, shouldn't she already know that it exists? How else did she get to Hyrule in the first place? If Zant sent her to Hyrule, then the question is now, why didn't Zant just take her prisoner in the first place? If he did try but she escaped, once again, how else did she get to Hyrule unless she used the Mirror of Twilight?
Maybe she didn't need it (though whether it's because of her headgear or whatever is a mystery), but someone from the light side would. Alternatively, maybe she was using it all along without realizing it, even with it broken, and it's just that someone from the light side who would need to stand in front of a fixed mirror in order to go there.