Zelda's Lullaby is played in the ending to send Link back to being a kid. But remember that Zelda talks about "returning to the way you were supposed to be" and such — playing Zelda's Lullaby by a shattered sign restores it to normal, so why can't Zelda's copious magic power do the same for Link himself? Talk about hiding your Foreshadowing well.
Zelda's Lullaby is Sheik's theme arranged slightly differently and at a different speed. The music was also in disguise.
This may be unintentional, but the third magic circle of Mars from the "Key of Solomon" looks somewhat like the Triforce. Its purpose is to cause discord that ensures the fall of one's enemy. When Ganondorf tried to take the Triforce, it split apart, and the separate pieces going to Link and Zelda is what led to his defeat.
Sheik (and many other Sheikah and Gerudo for that matter) can just disappear in a flash of light. She's actually throwing a Deku Nut — and then she disappears while Link is paralyzed.
If Link gets paralyzed by a Deku Nut when Sheik throws it, then why is he able to throw a Deku Nut and not get paralyzed? Answer: If you look at the animation of him throwing one, you can see he is covering his eyes when throwing it.
Many a player has got frustrated with Navi's apparently completely useless advice in the Great Deku Tree — "Yes, Navi, we know how to open a damn door!" Except that there aren't any buildings that have doors in Kokiri Forest… and if Link was left there as an infant, then he's never actually seen a door before, thus making Navi's advice… completely relevant and useful for him.
The rating 'E for everyone' is a little off since, let's be honest, there are things in this game that still can give a grown man a pretty good scare. Then it hit, Link is the holder of the Triforce of Courage, and true courage is only achieved when one conquers his own fears. So for a little kid playing this, they would be scared out their mind while playing this game to such an extent that they don't dare to keep playing any more, because it is so freaking scary at some parts. But daring to picking up that controller and meeting your fears head-on is truly courageous, and makes a worthy holder of the Triforce of Courage.
"Sheik" is an Arabic word for a tribal leader. Zelda (and by extension, Sheik) is the the ruler of the Sages. Sheik also claimed to be a member of the Sheikah tribe.
The "official" timeline released for the series indicates that all the games that were released before Ocarina of Time took place in a timeline where the Hero of Time was defeated by Ganon…but after OOT, we have games based on the two timelines where the Hero won the fight. The previous games were based on Link losing the final boss fight because you, the player, weren't there to guide him to victory. Winning the last boss fight in Ocarina of Time is actually the player themselves being able to Set Right What Once Went Wrong for the entire series. This makes more sense in the opening cutscene: Link had a dream of Impa riding away from Ganondorf with Zelda. Later on, Zelda thought Link's name sounded familiar. This means, after Link's defeat and Ganon's sealing, Zelda went back in time with the Ocarina of Time to Set Right What Once Went Wrong, but in the process, she may not remember everything due to the Triforce's completion (while she possesses Wisdom, she no longer has its possession). This also means due to Link having the Triforce of Courage, he was able to remember everything when he finally won his final battle with Ganon. This would also explain why Zelda was Properly Paranoid.
The King of Hyrule trusting Ganondorf is generally accepted (understandably so) as an Idiot Ball moment, but there is a kernel of justification for it: the Gerudo are a tribe of thieves (and kidnappers, at least in the future). It makes sense that the King would jump at the chance to have Ganondorf swear allegiance to him — an alliance with a king of thieves would potentially allow Hyrule to avoid becoming a victim of their crimes.
The existence of the 3D remake itself is fridge brilliance. Imagine yourself as a kid, playing through Ocarina of Time for the first time on a classic Nintendo 64. As a kid, games can be pretty hard, mostly because you're inexperienced and new to the activity. Now you're grown up and playing through it again on the 3DS. The game is easier than you remember, but also presents entirely new challenges in Master Quest. The whole concept mirrors Link in the story. He starts off young and inexperienced, but grows into his position and becomes an adult, solving problems that stumped him as a kid, but also overcoming new problems of his own along the way. In a way, the game itself went to sleep and awoke several years later.
Speaking of the 3D remake, one of the complaints with the game's first person aiming is that it's annoying having to turn the 3D off every time you use it if you want to use the rather accurate gyro controls without losing your viewing sweet spot. Until you realise that closing one eye, which is exactly what someone using a slingshot or bow would do in real life, achieves the same effect with much less effort.
When Link is an adult, there will be special ice that can only be defrosted with Blue Fire. This, at first, just seems like an aesthetic choice, but it makes sense that this blue fire is the only fire able to defrost that ice, considering blue fire in real life is hotter than red fire. Now, Link's method of getting that fire to the special ice is something else entirely.
The only catch is that it's described in-game as being a cool flame, so presumably we're dealing with "ice" that's somehow hot.
Whenever Link defeats a boss as an adult, he is transported via being encased in a transparent blue gemstone to the Sacred Realm so he can meet with the awakened Sage. Those same blue gemstones were used again by Agahnim to imprison the seven maidens in the Dark World (the corrupted Sacred Realm) in Link to the Past. No doubt he learned to use that same spell, long after the events of OoT took place.
The same fish that wins you the heart piece as a child will win you the Golden Scale seven years later. Same spot and everything.
Why does Link not understand Ruto's proposal to him? Because he grew up in the forest with a bunch of kids! He has no concept of "marriage"!
Dark Link doing a Blade Walk on Link's sword should he attempt to crouch-stab. Why counter this one move so specifically? But the Fearful Symmetry page puts the fight with Dark Link… alongside the one from Adventure of Link. It doesn't make sense from a chronological standpoint, but it looks like the game developers caught on to the crouch-stab trick from the NES port of Adventure of Link, and explicitly punished any veteran to Zelda who would think to try the same trick again here.
As soon as you get the Fairy Ocarina, you can play every single song in the game and then some, but they won't have any effect until you've "officially" learned the song. Why? Whenever Link completes a song, he plays a few notes past the ones you played on the controller. You can play the first few notes all you want, but it won't be the same song until Link learns the rest of it.
Given that they referred to Ganondorf as "great" and there didn't seem to be any particular difference made when to their lives when you clear the Spirit Temple, why do the Gerudo celebrate the fall of their king with all the other races? Well, it's mentioned by the Gerudo themselves that there were rumors of brainwashing experiments in the Spirit Temple which turn out to be true. The problem that was afflicting the Gerudo was a climate of fear. They had to voice their support of Ganondorf; a single word of dissent could mean being dragged off and forcibly converted into a mindless slave (i.e. Iron Knuckles) and would likely never regain their free will like Nabooru did.
Given this, there's also the possibility that if the Gerudo didn't agree with Ganondorf, and were siding with him strictly out of custom, (Something Narbooru heavily hints at), then its likely that they'll receive a pardon for aiding him, and be invited to live in Hyrule, a much more hospitable place than the desert. This is given even more credence because Zelda, who will likely be queen at this point, knows of Narbooru's aid and status as a Sage, will have the authority to do so.
Farore's Wind is the Goddess Spell that a lot of players don't end up using - it's just a quick teleportation that may or may not save you a couple seconds, compared to Din's Fire saving you a lot of trash mobs and Nayru's Love saving you a lot of hearts. Then you realize: Link, as the bearer of the Triforce of Courage, isn't going to back down. He's not going to run. Farore's Wind is the Goddess of Courage telling him to stop pushing himself.
The first three dungeons lead up to the Triforce. First of all, look at the Spiritual Stones. Don't green, red, and blue usually represent courage, power, and wisdom in the series? Heck, look at the dungeons' items. The slingshot represents courage because it charges headfirst without thinking. That's pretty brave if you ask me. The bombs need no explanation, they clearly represent power. The boomerang is wisdom because, instead of charging into situations, it finds new ways around problems and always returns to the thrower. Talk about Foreshadowing.
The Weird Egg that Malon gives you hatches into a chicken. Considering all other chicken-like fowl in-universe are called cuccos, an egg that hatches into a chicken really is a weird egg.
The medallions and their corresponding sages are pretty straightforward, save for perhaps that of Spirit. But thinking about it, that sage and medallion is related to the Gerudo tribe that lives in the desert. "Spirit," in this case could be synonymous with "willpower" or "drive." Who would actually have more willpower than a tribe that lives out in the desert, the harshest of environments?
Ganondorf's blood being changed from red to green is a point of contention for some because of the reason it was done. However, it actually makes a measure of sense when you think about it. Skin is translucent, and the color it takes is influenced by the color of the blood running through the body. Considering that Ganondorf in this game has a pretty noticable olive green skintone (a trait that is retained in the game's Updated Re-release), his having green hued blood isn't really all that strange.
The three timelines that split as a result of the game all have one holder of the Triforce remain in that timeline. Ganondorf, Triforce of Power, rules the timeline where Link dies to him and Zelda either joins him in death or is imprisoned.. Link, the Triforce of Courage, lives on in the Child Timeline, being away from both Zelda and Ganondorf. Zelda, the Triforce of Wisdom, oversees the remnants of the Adult Timeline, with Ganondorf sealed and Link sent back.
How does that make them cannibals? If anything, they're drinking water that's been infected by corpses and rotting flesh. Which is pretty gross, sure, but it's not cannibalism.
The Deku Tree Sprout revealing to Link his origins. Sure, it might sound like a motivation or destiny, but it could be a lot for Link to take in, seeing how he believed he was a Kokiri all his life.
Why would the NPCs have HEARTS of all things in their pots/chests? Think about it.
Stay in Hyrule Field during the night, and wherever you go, an infinite amount of Stalchildren start clawing their way out of the ground to attack you. So apparently, most of Hyrule is actually a mass grave where the angry dead are just waiting for a chance to get ahold of anyone wandering around. Worse yet, a mass grave of children. Then you remember there was a civil war just ten years prior…
One possible translation of "Kokiri" from Japanese to English is "child killer" — it fits with the Hylian fear of the Kokiri Forest, but what does that say about the Kokiri children themselves?
All of Hyrule's water comes from Zora's Fountain. King Zora has the proud distinction of sitting on said water... Combined with Kakariko's "cannibal well," one has to question the cleanliness of Hyrule's waterways.
The water in Zora's Domains flows directly through a tunnel into Lake Hylia. The rest of Hyrule gets its water from the Sleepless Waterfall, which feeds the river directly from Zora's Fountain. Although, that water is also occupied by a...fish-whale-god-thing, so your point still stands.
Waterfalls are natural water purifiers. Survivalist knowledge says that if you have a choice between taking water from the river or from the fall, you go for the fall.
After clearing the Forest Temple, you learn that there was a bloody civil war in Hyrule around the time Link was born. While the length of the war itself is not known, it is fairly recent. The backstory told is the only time in the game that you get to hear about the war since no one else will ever talk about it. Either the war was so terrible that everyone simply forced themselves to forget it or someone (or a group of people) did something that made people forget. While subtle, the after effects of the war are still present in the gorons and zoras; they live in isolation and will question why you are visiting them while others will refuse to talk to you unless you show your proof of connection to the royal family. It's possible that the races of hyrule haven't quite made up with each other just yet, though the hostilities are not present thankfully.