The Legend of Zelda: The Wind Waker/WMG

Feel free to add theories about whatever you like

The three swordsmen on Outset Island represent the Triforce in total

 * Orca represents Power. He spends all his time either honing his own physique, or training Link in the ways of the sword.
 * Sturgeon represents Wisdom. Retired from swordplay, he spends all his time in careful study. He outright states that he wishes to imbue Link with wisdom.
 * Link, obviously, represents Courage.
 * Orca considers Sturgeon a weakling and an embarrassment for not maintaining his physical prowess and spending all his time with books. Sturgeon considers Orca a roughian and a Jerk Jock for spending all his time working out and carelessly breaking Sturgeon's belongings with all the commotion. The two embody what happens when one's life is out of balance, showing that both "all brawn and no brains" and "all brains and no brawn" are paths leading to frustration, anger, and even broken families. Link, on the other hand, learns valuable lessons in Power and Wisdom from them, and balances them with his own Courage to prove himself worthy of being the next Hero.

Tingle is a Death Eater

 * Seriously, look at what's on the back of his green outfit. It's a picture of a cobra about to strike! (When I discovered this, it was during the stormy Endless Night chapter of the game, which made my Fridge Horror even worse.)

The sea and Hyrule are located in an alternate Earth

 * The constellations are the same as in Real Life. That's enough to guess it.

Windfall is the remains of the Hyrule Castle from Ocarina of Time

 * If you look at the town's entrance, it looks similar to the barred gaurd gate you use to sneak inside to meet Zelda, also The buildings may have been built from the same materials as the castle itself. It also seems to be where the castle town was.
 * But the whole castle is underwater.
 * I think this person Meant the Original Castle, Since Hyrule Castle seems To be Rebuilt every game.
 * I think the person you're responding to means that you actually visit Hyrule Castle, and it's underwater, well south of Windfall, so it can't be the remains of it. Note that the area around Hyrule Castle strongly resembles that around Hyrule Castle in Ocarina of Time, too, so it's not a rebuilt castle in the meantime.
 * More likely is that Windfall is the remains of Kakariko Village, not too far from Death Mountain, which would be Dragon Roost Island. The alternative conclusion is that the Castle was actually moved to where Lon Lon Ranch was, which could explain the similar geography, and accurately place Kokiri Forest/Forest Haven, Death Mountain/Dragon Roost Island, Gerudo Fortress/Forsaken Fortress, and possibly Lake Hylia/Outset Island.
 * It's highly unlikely that Windfall is the remains of Hyrule Castle from Ocarina of Time. The Wind Waker takes place in the adult timeline, where Adult Link defeated Ganondorf and ceased to exist when he was sent back to the past. The relevance of this is that Ganon destroyed Hyrule Castle, so it no longer exists as of TWW for anyone to build on it. (This incidentally is also why a new castle was built elsewhere in Hyrule after Ganon was sealed in the Sacred Realm and presumably Zelda took the throne.)

Fire Mountain is part of the Death Mountain range

 * It is a hot spot that is constantly moving, seeing how Dragon Roost could be Death Mountain but is not as active as before, it could be the Zelda equivalent of the Hawai'i Islands.

Lenzo is Link's grandfather.

 * When you're in the photo shop at Windfall Island, you can see the photographs Lenzo has taken and get commentary from him as well. When you come to a picture of Outset Island, Lenzo says something like, "When I was but a lad, I met a beautiful young girl there. Although I suspect she is not as young as she once was...". The young girl he means was Link's grandmother when she was only 18 or 19. Lenzo was the same age, and they were young lovers. He left a few weeks after he met her, and nine months later she had Link's mother (or father).
 * This troper is speechless...

Outset island is the remains of Lake Hylia waterfront.

 * The gap between the two islands is the path that lead to Hyrule Field, also Aryll's lookout appears to be built from the remains of the lakeside laboratory, specifically the tower you can access via magic bean.

The Forsaken Fortess once belonged to the Sheikah

 * Take a good look at the entrance to the Ship perched on top: there are Sheikah eye symbols on the door!
 * It could be a coincidence, though, since there seems to be only a vague resemblance...

Ganondorf isn't sealed permanently
Chances are the magic of the Sword and his own magic are going to preserve him rather well, so he won't erode. Eventually, somebody is going to decide to try looking for sunken treasure in the ruins of Old Hyrule, and dredge up this weird statue of a Gerudo with a sword in it... and then its just a matter of waiting until someone or something manages to convince a Link that he needs the now-available Master Sword.
 * When the Master Sword gets sealed in something, isn't it normal for the sword to be unpullable except by a chosen hero? So if anybody is going to pull the sword out of Ganondorf, it's going to be a future Link, and Ganondorf's track record against people named Link is miserable.

Windfal island is kakariko village.
it's near dragon roost island, rumored to be death mountain, and it has a windmill, just like in Oo T, it's the main town, just like it was for most of Oo T, and it's music has a few points where it' sounds like kakariko village's theme in Oo T. the only question is how it didn't end up underwater. perhaps kakariko is higher up than we thought?

The Queen of the Great Fairies is Fi.
An obvious one really. The Queen looks quite a bit like a younger version of Fi (or more accurately, Fi is an older version of the Queen), but since they're both Really 700 Years Old, it doesn't really matter. Perhaps, after they flooded Hyrule, they drew Fi out of the Master Sword (Ganondorf killed the two Sages, so it was already de-powered anyways), and made her the new Queen to help the next hero that would inevitably appear. (And if the new appearances of the other Great Fairies in WW isn't a straight-up Art Shift, perhaps Fi recreated them in the interim.) She even says that she likes Link when they meet, probably because he reminds her of her old master.

Location, Location, Location
In between Ocarina of Time and The Wind Waker, there was a Great Flood, which turned Hyrule into the Great Sea. Although most of it was underwater, many of the islands and locations seem to be remnants of the drowned kingdom. (And as for how those places became islands instead of staying underwater - the Goddesses raised them up.) "Once upon a time, long ago, the Koroks took on human forms, but when they came to live on the sea, they took these shapes."
 * The Gerudo Fortress = The Forsaken Fortress
 * Castle Town = Windfall Island
 * The architecture on the island seems to resemble a castle. The resemblance to Kakariko Village is due to the residents of Kakariko moving to Windfall and rebuilding their homes. Eventually, the sub-cultures/architecture of the people from Castle Town and Kakariko Village merged, and they created Windfall.
 * Death Mountain = Dragon Roost Island (& Fire Mountain)
 * In Twilight Princess, it’s implied that the Gorons don’t need to breathe, and can stay underwater indefinitely. So most of them may have felt no need to evacuate to higher ground when the Flood came. (The three travelling merchants - all clearly Gorons - located on Greatfish Isle, Bomb Island, and Mother and Child Isles remain on the surface for business purposes.) So the Gorons stayed in Goron City.
 * The Zoras, on the other hand, despite being highly adapted to aquatic environments, weren’t so lucky. Although they seem at home in the water with their fins and gills, their humanoid bodies imply that they aren’t meant to be in the water all the time.
 * In real life, most fish are meant to be in either saltwater or freshwater; only a few, like bull sharks, can swim and breathe in both. Some of the Zoras, by praying to the Goddess Nayru, were able to adapt quickly to the saltwater environment, and settled on Greatfish Isle . To thank Her, they created Nayru’s Pearl, which housed some of power of the Goddess Herself. They also hatched, nurtured and raised Lord Jabun, the offspring of the demi-god Lord Jabu-Jabu, to watch over them as the new living Water Spirit.
 * The other Zoras travelled north to the top of Death Mountain, and turned to the Goddess Din for aid. In answer to their prayers, She gave them avian features (beaks, feathers, wings) to protect them from the scorching heat, and entrusted a dragon egg to them. This egg held the single surviving offspring of the dragon Volvagia, who was slain by the Hero of Time. When the egg hatched, Din deemed the newborn dragon to be Lord Valoo, the living Sky Spirit. The Zoras, no longer being Zoras, began to call themselves Ritos, in memory of Ruto, the Princess (and later Queen) of the Zoras in ancient times.
 * Although the Ritos had wings, their wings were not big or strong enough to enable flight. So Din instructed Valoo to give each adult Rito one of his scales (which grew back easily). These scales triggered a magical “growth spurt” that caused a Rito’s wings to grow big enough to allow flight. Eventually, it became customary for young Ritos to visit Valoo and receive their wings when they came of age. To thank the Goddess for Her kindness, the Ritos created Din’s Pearl, which housed some of the power of the Goddess Herself.
 * Kokiri Village & The Lost Woods = The Forest Haven & The Forbidden Woods
 * When the Great Flood came, the Kokiri were completely unprepared. They were afraid to leave their forest, and couldn’t bear to abandon their guardian, the Great Deku Tree. The Deku Tree, who had just reached his juvenile stage of growth, prayed to the Goddess Farore for aid.
 * The Goddess answered by taking away the burden of the human forms the Kokiri took on. They shed their mimicked humanoid features and became what they had always been underneath: the Koroks.
 * The Kokiri, despite their mammalian appearance, had always been sentient plant-people. Instead of blood, they had chlorophyll keeping them alive. When they became the Koroks, they became lightweight enough to use the leaves that the Great Deku Tree shed as makeshift “wings”.
 * To thank the Goddess for Her kindness, the Koroks created Farore’s Pearl, which housed some of the power of the Goddess Herself.

--The Great Deku to Link, when the Koroks reveal themselves.

Nudge is a Shiekah

 * Nudge is Zelda's confidant and the strongest of the pirates. In the ancient portrait in Hyrule Castle his ancestor was the only female attendant. This attendant was the Impa of that time, another nurse maid and bodyguard. Now Nudge fills in the Impa role of sworn protector and lancer.