The Legend of Zelda: Skyward Sword
The Legend of Zelda: Skyward Sword
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An early concept-art shows a version of Skyloft that was actually inspired by the real-life Mont Saint Michel in France.
Contributed by ChocoPain
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Rupin, the owner of the gear shop in Skyloft, has similar personality and physical traits to that of the Happy Mask Salesman from Ocarina of Time and Majora's Mask. Both have similar facial expressions, have mood swings and both are owners of shops. It could be implied that Rupin in an ancestor of the Happy Mask Salesman.

Rupin's name is also a pun on "Rupee", the currency used in almost all Zelda games.
Contributed by Boyobmas
In early trailers of the game, Fi was not implemented. Link also seems to have the Master Sword and Hylian Shield, which the player can get later in the game.
Contributed by Shiny Blazeikin
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The box art for the game was changed when it was localized to North America.
Contributed by Ophl
The Goddess' Harp played by Zelda Spoiler:(and eventually Link) is the same harp used by Sheik in Ocarina of Time.
Contributed by Takahashi2212
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According to Hyrule Historia (pg. 23) "it was decided that all residents of Skyloft would be modeled after birds." This explains why some of the Skyloftians have bird-like names and features themselves, such as Groose's cocky attitude and his hairstyle that resembles a rooster's comb.
Contributed by zybershield
When talking to the little girl Kukiel right after meeting Batreaux in Skyloft, she will say that he told her that "it's too dangerous to go out alone" at night, referencing the iconic phrase "It's dangerous to go alone", said by the old man who gives Link his sword in the original Legend of Zelda on the NES.
Contributed by ThatFlint
Before the Kikwi Hermit tells Link where he can find the flame, he says "All right, I'll tell you. But remember - it's a secret to everybody", referencing the phrase "It's a secret to everybody" from the original Legend of Zelda.
Contributed by Charlie
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In the Skipper's Retreat, there is a reference to the film Titanic. In his cabin of sorts, there is a painting of two robots in the front of a ship,one holding one out with it's arms out. A parody of the famous scene in Titanic, when the main characters Jack and Rose, do the exact same thing.
Contributed by JzillaMerida
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The characters' Loftwings all have feather plumes matching their respective rider's hair style.
Contributed by oozy the wolf
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Gratitude Crystals from Skyward Sword and Star Bits from Super Mario Galaxy are based on candy. The candy is called Konpeitō and is popular in Japan.
Contributed by DidYouKnowGaming
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Skyloft contains a hidden area filled with Remlits (a species of small cat-like animals). This area is near the Goddess Statue and is only accessible after obtaining the Clawshots.
Contributed by JzillaMerida
After completing the Thunder Dragon Quest, if the player talks to Golo, the Goron outside of the Lanayru Mining Facility entrance, at least twice, Golo tells the player that he is jealous of his discovery. From this point forward, the game becomes impossible to complete and the events at Eldin Volcano and Faron Woods will no longer occur.

Nintendo has since tried to fix this glitch by releasing "The Legend of Zelda: Skyward Sword Save Data Update Channel", a free channel from the Wii Shop.
Contributed by PheonixGRX
Skyward Sword had the longest development period of any Zelda game.
Contributed by Petie
Playing the song Ballad of the Goddess backwards results in the melody of Zelda's Lullaby being heard. Alternatively, reversing Zelda's Lullaby will yield a simplified version of Ballad of the Goddess.
Contributed by Petie