Terrors of the Sea:
While you're at sea, you'll run into patches of enemies. Everything from sharks, to octopi, to pirate patrol boats that will launch cannonballs at your ship. You can fight back with weapons like your boomerang or bow and arrow. You can also equip your bombs, which will mount a canon on your ship to fire your own shots.

Fishman the Fish:
Not all the creatures in the great sea are out to destroy Link... The sea is full of friendly fish. There's one of these fish for every square on the map. You can see them splashing in the water as you're sailing, so keep an eye out for them. They'll not only give you a map for the current section you're in, but they give you tips and advice about the game. To attract a Fishman to your boat, you just need to approach one, and toss out some All Purpose Bait.

There Be Treasure!
The floor of the great sea is home to many sunken treasure chests. First up, is the small chest. You can find up to fifty rupees in one of these. Just find small circles of shining light on the surface of the sea. Sail to these locations, and use the grappling hook to pull up goods from the bottom of the sea. These are the most common types of treasure chests.

Bigger Treasure:
The second kind of treasure is found with the many treasure maps scattered throughout the land. After collecting a treasure map, compare it with your navigation chart to figure out where the treasure is located. Sail to that area, and you'll see a higher bright beam of light coming from the bottom of the ocean. Pull up the sunken treasure to find heart pieces, and valuable rupees. There are many treasure maps to be found.

Friendly Fairies:
There are several Great Fairies on various isles throughout the Great Sea. Each one of them has a magical spell that they can grant to Link... If he can manage to find them. Check the Fairy Fountains page for information. You can also use fairy fountains to stock up on bottled fairies before you head into battle.

Ballad of Gales:
You spoke with a strange blue frog when you learned the first song for the Wind Waker... But the brother of this frog controls cyclones out in the sea. After you get the bow and arrow, you can learn a song to warp you all over the map. If you find a really big cyclone, this pink frog will be inside controlling it. If you can manage to hit him with three arrows, he will teach you the Ballad of Gales.

Old Man Ho Ho:
This crazy old man is armed with a telescope... He's found in several different locations, always looking at something of interest. He'll give you hints about different things that you can explore. For example, he can be found perched high up on Outset Island, looking at a huge rock. Later on in the game, Link can use the Deku Leaf to fly across there, and use the Power Bracelets to lift the rock and find a secret cave...

Screenshot by Siberian Guard

Salvage Corps:
These devoted divers can be found floating on their boat in many places throughout the Great Sea...
If you stop and talk to them, they'll give you a Treasure Chart that they've found. It's not what they're looking for. They're after BIG treasure... Something about a legend of mysterious "Triumph Forks". Later on, they'll give you some rupees that they've found at the bottom of the sea.

Screenshot by CommanderJinx

Submarines:
These wooden vessels are found partially submerged, and scattered over the great sea. Inside a submarine, you'll find swarms of enemies. Destroy all the enemies, and you'll score a treasure chest. Inside the chest will be various things, from Treasure Charts, to Rupees, even a Piece of Heart.

Big Octos:
These giant creatures hide underwater. You can detect a giant Octo by noticing a flock of seagulls flying in a circle. The areas where Giant Octos are located can be found on the Octo Chart. When you're on land, look out onto the sea with your telescope until you find a bunch of seagulls. Fly straight into them, and a Big Octo should appear to challenge you. You need to shoot out all of an Octo's eyes to kill him, using the Boomerang, Arrows, or Bomb-cannon. Don't take your sweet time destroying the eyes though - You'll gradually get sucked in closer, and if you don't pop all of his eyeballs in time, you'll be swallowed and launched to a random spot of the map.