Anyway, the reason I'm making this thread is that I'm hunting around the net for resources that I would be able to incorporate into the setting. I plan to allow them access to Lizardfolk and Yuan-Lie, which have decent homebrew statblocks on D&D wiki. Along with creatures like Sahuagin and even Illithids (scoff if you will, though I plan to reflavor them quite a bit as non-abarrants who don't eat brains and have slightly more downplayed psionics). I'm also searching for things such as different ways to do about aquatic combat, sea-faring vessels, anything else I could use as inspiration, tips for making maps, tips for homebrewing the things I need to, and anything else from the net that might help me build the setting to the extent that I would like to.
saveordie.info/?p=249
Aquatic Combat
4.0 DU158 Sea Reavers of the Shrouded Crags
- This adventure has a submarine
3.5 Stormwrack
- Has detailed information and descriptions on various types of both realistic and fantastical watery environments, including underwater, the open ocean, ships, coral reefs, grottos, swamps, and such. Watery hazards such as waves, storms, exposure, rain, and the like are deeply explored.
- Basically the same as above
Sea-Faring Vessels
- Many of the ships are water capable (personally I have been using the Hammership as the de facto ship in my campaign since I bought the box set)
Ideas
Aquarius Mission by Martin Caidin
- Deals with the finding of an underwater race and protected it form Mutant sea life (Far Realms hook)
Night Below: An Underdark Campaign
- Great plot with Aboleths. Just remove or mod the surface aspects.
- Player’s travel through a monster-infested swamp to get to the city, which is being slowly swallowed into the sea. Qagmire (one of three towns) is a whelk-shaped "spiral city", built by a dead race.
- Takes place both on and beneath the surface of the sea, and includes rules for underwater play[Basic Edition]. The module also includes a description of the war rafts and the underwater city of Colhador
GAZ4 - The Kingdom of Ierendi
- Describes the island realm of Ierendi, a pirate-ridden archipelago that tries to appear as a tropical paradise
GAZ9 - The Minrothad Guilds
- Describes the great trading guilds of Mystara and their island homes
- Player’s flee the evil city of Flotsam, crossing the Blood Sea (and maelstrom), where they may encounter Istar the City of the Deep and become involved in an undersea battle.
C3 - The Lost Island of Castanamir
- A mysterious island connected with a number of recent shipwrecks and disappearances.
U1- Sinister Secret of Saltmarsh, U2 - Danger at Dunwater, and U3 - The Final Enemy
- Pirates, Lizardfolk, and Sahaugin (oh my!)
- Explores the mentality and lifestyle of pirates, including an explanation of what is piracy, a history of piracy in the Forgotten Realms setting
Sea of Blood, Evil Tide, Night of the Shark, and The Sea Devils
- Everything Sahaugin
3d battle mat made from Plexiglas. The will give the player’s the feeling of being floating through encounters.
Besides the expense of sea travel, mysterious seas, and creatures of the deep; the player's were hindered by politics of the various islands. During the campaign the various players gained control of the islands, developed their own governments and laws. They struck bargains and forged alliances with each other. First forming two empires and finally joining (under protest) together. At the end of the campaign they had finally returned to the lost continent, which was the premise of the campaign. It took the players 26 years.
... I'm hunting around the net for resources that I would be able to incorporate into the setting.
In addition to morandir62's most excellent list, you might look for Alluria Publishing's quite comprehensive Cerulean Seas supplement for Pathfinder. Pathfinder's Advanced Players Guide also has a handful of aquatic references. While my current 3.5e undersea game have been running for over three years, I'm considering a Pathfinder/Cerulean Seas game run via MapTool/Skype.
You might also look for Discovery's Blue Planet video series, available on iTunes and a book called "OCEAN" (DK Publishing), as I have found them to be excellent sources for inspiration.
Another thread with lots to look over: http://community.wizards.com/go/thread/view/75882/19557726/Underwater_Campaign
I don't recall seeing any water world settings on this board, but I would not be surprised if you dug deep enough into the workshop you could find another similar project 
www.wizards.com/default.asp?x=dnd/we/200...
THE DRIFT PORT OF SHADOW
Civilization. Elman the Explorer stared at the cluster of old ships lashed together to form a floating town.
"Do you think they will have sufficient Food to allow us to make the journey to the forgotten City?" Elman turned to his Second.
"We can only ask, and here's hoping that they dont slit our throats for what little we have."
DM Briefing: The Drift Port of Shadow is one of those few clusters of civilization that struggle to survive since the Tide came in permanently. It is a Floating community made of old ships lashed together to form a large island. The people are hungry and poor and survive by taking from others.
THE LAPIS LAZULI TOWERS
The old timber ship moved between the lapis lazuli towers under the power of its oarsmen alone, the blood-red sails now emptied of any breeze that might have fuelled them. Bridges held aloft by art alone strained between their distances.
Elman the Explorer noticed something that the others did not. An increasingly many something’s that seemed to shadow their passage, drifting amongst the peaks of the tallest towers as their vessel moved forward with every stroke.
"Softly to the ballista Mister Ganel, we have predators above us in the battlements and eaves." His second moved away slowly to relay the order to the other crew.
DM Briefing: A city is flooded by increased ocean height. Though the towers extend a hundred feet or more above the Water they have already sacrificed an identical distance below the surface.
The Seaweed Fields
The Seaweed Fields are an undersea regions located near the coast line, usually on rocks or a reef. Seaweed is a type of stringy algae that comes in different colours such as: red green and brown. A seaweed grove is never very deep, as the sun is required to allow photosynthesis for it to grow. Fish and small herbivores often feed off the algae and predators will often wait in deeper seas close to the seaweed beds. The Hemes Arbora, farm seaweed as their main source of food.
The Giant Oyster Trench
The Trench of the Giant Oysters is an underwater location on the Carrivar near the equator. As its name implies, the seabed of this region is populated with oversized mollusks, luminescent flora and fauna. Varying species of eels as well as the Sea Leviathan live deep within the trench. Other monstrous creatures populate the trench; refer to the section on beasts found on Carrivar. The equators trench is 10 km deep and ranges from 30 km to 70 km wide. The giant oysters ring the upper section of the trench close to the light rays that penetrate the water. A giant oyster can grow as large as 4 metres wide and has a hard white shell. Pearls can be found in the oysters on rare occasions, but the true worth of the oyster is its flesh. The Hemes Arbora will go to great lengths to capture a giant oyster as a test or trial of tribal prestige. Refer to the giant oyster stat-block should the player characters try to kill or take a pearl from the oysters.
Hemes Arbora Underwater Village
The Hemes Arbora village is a collection of huge ocean seed pods linked by a string of vines. Luminescent coral and algae, is used to light the interior of a pod. Each seed pod has a hard outer surface that helps protect the Hemes Arbora from predators. As a general rule an underwater village is situated under low hanging rocks or in a location that provides protection from colossal creatures. A village is usually made up of a shaman, and between 100 to 250 Hemes Arborains.
Lost Temples Princesses Quarters
The Princess Gree is a high cast Hemes Arbora shaman who lives in a gargantuan sea shell. Gree is the spiritual leader for many of the Hemes Arbora, but has separated herself from the tribes. The Princess is gifted with a strong link to the light side of the force and many sea creatures protect the sea shell temple. Twenty Hemes Arbora warriors guard Gree, so gaining access to the shaman is very difficult. Gree is wise beyond her years and sees the future of her race journeying through the stars.