The music in that part also has parts of Zelda's Lullaby, the Clock Town theme from Majora's Mask, the title theme from The Wind Waker, and the Hyrule Field theme from Twilight Princess. And the orchestra music part was also originally composed for Twilight Princess, though never previously used in-game.
In a nod to the entirety of the series, the yearly ceremony at the start of the game happens to be the 25th one.
Also, when you meet with the Thunder Dragon, he offers to add serial numbers to your name just like his robots. Namely Link-16, as this is the sixteenth Zelda game if the non-canon CD-i titlesare excluded.
The main melody of the Ballad of the Goddess is actually Zelda's Lullaby played backwards, which is actually somewhat spoilery if you deduce it, as Zelda is a human incarnation of the Goddess.
His other, less powerful form is ressurrected as a giant, mindless, rampaging beast. In the Oracle games, Koume and Kotake were only able to ressurrect Ganon as mindless, rampaging beast.
Beedle's ancestor makes an appearance, with the same theme from The Wind Waker and the same grunt when you come in. He also runs the shop from the sky that can only be entered after getting his attention (in this game, by firing a weapon at the bell to get him to lower a rope)... Sound familiar?
In the Silent Realm, you collect tears in a container identical to the one in Twilight Princess.
The Silent Realms themselves are quite similiar in concept to the central temples of Phantom Hourglass and Spirit Tracks, with invincible guardians and sentries who will alert those guardians if they see Link and who can kill Link in one hit.
The entrances to a good number of the dungeons dip downward in a manner reminiscent of the dungeon entrances from the first game. The Ancient Cistern's entrance even looks like a mouth, or to be more specific, a fish's mouth. Angler Cavern and the Catfish's Maw from Link's Awakening immediately spring to mind.
A chronologically later game showed that there are, in fact, two Temples of Time. The main one is in Lanaryu Desert, which looks to be in the same location as Arbiter's Grounds. The second one is in Sealed Grounds, which is in the same place as the Lost Woods. The past version of Twilight Princess' Temple of Time at the top floor is eerily similar to where you get the Master Sword in this game. Piecing this all together, the island where you get the Master Sword was bound to drop at some point.
Hyrule Historia even confirms that the Temple of Time seen in Ocarina of Time and Twilight Princess was built over the ruins of the Sealed Temple.
The surface's provinces are named after provinces from Twilight Princess, with at least one corresponding to a sub-area in TP (Faron Woods).
The first item you get in the game is a sailcloth, and you use this in tandem with Link's Loftwing, which is red. In The Wind Waker, you had to find a sail for the King of Red Lions, a boat you use to travel in the game's overworld.
The sailcloth works very similarly to the Deku Leaf.
The Skyloftians acquire their Loftwings in a very similar manner to the Kokiri and their fairies.
The bottom of the boss room in the Lanayru Mining Facility has a turn table and trains in a manner similar to the Tower of Spirits in Spirit Tracks.
The Symbols of the six sages can be found on the arch leading up to the Goddess Statue and the Sealed Grounds.
Zelda has a Tingle plushie in her room.
The Gust Bellows is similar to the Gust Jar from The Minish Cap, as are the Mogma Mitts to the Mole Mitts.
And, one to the very first game: "It's a secret to everybody" is uttered by a Kikwi hermit. It's also said by a Parella.
The pit of bones in the Ancient Cistern have a striking resemblance to similar rooms in the Shadow Temple in OOT.
The intro sequence is very similar to the one from The Wind Waker, narrating a legend that forms the backstory of the game, depicted in an ancient art style (medieval art for The Wind Waker, cave paintings for Skyward Sword).
Not to mention that the stories are very similar: The land was idyllic before, but an ancient evil rose from the earth, conquering the land and making life miserable. The people prayed for divine intervention, they got it in the form of sealing the evil away in the land below while the survivors went on to live on islands above it.
A more subtle one is that in Majora's Mask the player could give the hand a few different pieces of paper, one of which is a letter between two lovers. Here the only piece of paper you can give the hand is a love letter.
The animation of the Triforce assembling itself is oddly similar to a another Triforce animation in the intro of A Link to the Past.
The boss of Ancient Cisternrequires you to pick up his sword and slash him, a call back to using monster's weapons in The Wind Waker.
The Master Sword before it is blessed by Zelda looks very similar to the unempowered Master Sword from The Wind Waker, with the wings folded in.
When Link defeats the Imprisoned, the effect used is the same as when a Twilit enemy is killed in Twilight Princess, followed immediately by the animation that plays when the remains of a boss would be pulled together to form a fused shadow/mirror shard.
The miniboss fight in the Earth Temple (a fire-based temple where you earn the Bomb Bag) is two Lizalfos, with the room being made up of many hexagons, much like the miniboss room in Dodongo's Cavern from Ocarina.
Loftwings are the birds always depicted on the Hylian shield and other Hylian designs. Of course, like the emblem on the shield, Link flies a red one.
Link's reaction to touching lava - leaping into the air with the seat of his pants on fire - is the same as Toon Link's. Contrast the more realistic actions when he drowns in water or sand.
Impa appears as both the young guardian, ala Ocarina, and an old, blue-cloaked advisor like in Zelda II.
After the third dungeon, the Big Bad nearly gets Zelda, but she escapes thanks to Link and Impa and throws Link the magical instrument of the game, just like in Ocarina.
If you throw one of the pots in Skyloft close to a person, they will jump and be startled for a second. Fledge's animation really looks like the guy you have to scare in the café in The Wind Waker (by throwing down pots, too).
The ability to grab rupees and hearts with your sword returns from games such as the original and the Game Boy ones.
At the end of the game, Zelda asks what do you want to do. This is similar to Spirit Tracks which had Zelda asking what did you want to do after everything was over near the end of the game as a branch for the game's multiple endings.
Near the end of the game, Ghirahim prepares to sacrifice Zelda to Demise, and the ritual looks a lot like the one used by Agahnim when he sacrifices the Maidens to break the seal on Ganon, complete with levitating victim.
The way Fi leads you to the Goddess Sword for the first time is very reminiscent of following the ghost of Darmani in Majora's Mask.
Professor Owlan, with his white hair and dark skin, looks similar to the Rito tribe in The Wind Waker.
The people who hang out at the Lumpy Pumpkin somewhat resemble the group that hangs out in Telma's Bar in Twilight Princess.
The recurring symbols in each of the three sections of Hyrule are the icons used to represent songs in the Oracle of Ages.
More importantly, they're the symbols of the Three Goddesses: Din, Farore, and Nayru.
Like Oracle of Ages, said songs are played on a harp.
Throwing bombs into baskets is a common way to progress during the Lanayru region. The idea was first used in a mini-game in Majora's Mask, and throwing a bomb into a basket held by a statue to knock it down was used in The Wind Waker.
At the beginning of the game, Zelda acts similarly to Marin from Link's Awakening, being a cheerful girl who plays the harp, lives on an isolated island, and wants to explore a part of the world that is blocked by a barrier and is considered by most people to have nothing worth seeing even if they could reach it.
Similar to the above, Groose has a lot in common with Ralph; both are rather obnoxious, have strangely styled red hair, and have intimate feelings for the local harp playing girl that has a special connection to one of the Goddesses, and due to this feeling become a rival of sorts to Link, until they loosen up later in the game and come to respect Link.
Once again, Link has to collect tadpoles that double as musical notes and teach him a song.
The fighting system in the game, while more directly inspired by Wii Sports Resort's swordplay modes, is also similar to how you fight many enemies in Zelda II: The Adventure of Link, as you have to attack from the right position to get past the enemy's defenses.
Using the Beetle is pretty much identical to controlling seagulls in The Wind Waker.
Planting a bomb next to a Shiekah Stone will cause it to blast off into the sky, similar to Ocarina of Time's and Majora's Mask's Gossip Stones.
The way that the pieces of the Triforce restore your life energy when you obtain them is very similar to how the shards of the Triforce of Wisdom did the same thing in the original game.
The conclusion to the Thunder Dragon quest is similar to two parts of Oracle of Ages: you have to plant a tree in the past then travel forward in time to when it's full grown, and you find a character dead in the present who you then have to cure of his illness in the past.
Link is starting to develop a history of getting violently shaken by another character. First the Happy Mask Salesman in Majora's Mask, later Linebeck in Phantom Hourglass, and this time around it's Groose.
Just like in Ocarina of Time, our first introduction to Link is seeing him have a nightmare about the Big Bad.
When you rescue the Mogmas from the Fire Sanctuary, their dialogue is similar to the carpenters you had to rescue from the Gerudo Fortress in Ocarina of Time.
When you collect the final Triforce, the Silent Realm takes on a golden hue before you leave...in A Link to the Past, where was the Triforce said to have been kept in the backstory? The Golden Land!
Ghirahim's cloak has a similar design to the Gilded Sword. This is either this or a major coincidence, considering that Ghirahim is a sword.
You get an item from a high place in a building by running into the wall and knocking it down, like you get the book from the library in A Link to the Past or Link's Awakening. The building's owner is not happy about this.
At the end of the game, Fi, who has become the Master Sword, has her consciousness fade into the blade, and enter a deep, eternal sleep. In other words, the Master Sword sleeps again, forever. The line itself is never said, so it is more of a stealth gag, if it was intended at all.
A minor one, with reference to the race names - aside from the Gorons making their usual appearance, there's also the Kokiri - I mean, the Kikwi.
ContinuingtheLegendofZeldatraditionofcertainrockformations, Spectacle Rock makes an appearance for the first time since Twilight Princess. However, unlike every other game it's been in, it is not seen in a playable area of the game, but only as part of the Eldin Province art on the map screen, where it sits between the Eldin Volcano and Volcano Summit statue points.