Ocean Punk

Also could be called Pirate Punk, though the setting may not even have so much as a single pirate in it in many cases. Life in a mostly watery world (or a mostly watery part of the world where the rest isn't of much matter) with distant islands connected by trade routes, ships sailing back and forth, and of course, many Pirates and buccaneers, whether they're wielding cutlasses on sailing ships or the aquatic equivalent of Humongous Mecha. May contain Organic Technology, and have a large focus on what happens under the waves as well as over.

This may also be a type of After the End setting, if the writers are trying to teach An Aesop about global-warming.

For a similar setting that trades the water for the skies, see Sky Pirates. And since Space Is an Ocean, you might have Space Pirates. Compare and Contrast its exact opposite Desert Punk.

Anime and Manga

 * One Piece
 * Blue Submarine Number Six
 * Future Boy Conan
 * Daphne in The Brilliant Blue

Film

 * Waterworld is definitely the aesop version.
 * Pirates of the Caribbean, natch.
 * Kamino in Attack of the Clones.

Literature

 * Ursula K. LeGuin's Earthsea Trilogy setting.
 * Settings like these may be in part inspired by the story of Noah and other 'great flood' stories from folklore and mythology.
 * The Robin Hobb Liveship Traders series
 * Except that the C plot (Malta) takes place almost entirely on land. Plot lines A (Althea) and B (Wintrow) certainly qualify, though.
 * The Scar by China Mieville
 * Tranquilium starts out overwhelmingly maritime, with the human population being concentrated on islands of various sizes.
 * The parts of John Birmingham's Without Warning that deal with the crew of the Aussie Rules.
 * Taylor Anderson's Destroyermen series is set in the Pacific Ocean of an alternate Earth where that pesky asteroid never wiped out the dinosaurs so it qualifies. Since the main characters are the crew of a WWII era destroyer that ran afoul of a time-space rift it also has elements of Diesel Punk.
 * The second Pendragon novel, The Lost City of Faar, takes place on the territory of Cloral, which is covered entirely by water . Cloral has generally advanced technology, including water guns that can blast through walls, plastic made from processed water, and water-based propulsion systems, with specialized floating cities called "habitats" housing residents.
 * Vampirates.
 * The Wave Walkers trilogy by Kai Meyer.

Live Action TV

 * The Crystal Maze replaced the Industrial Zone with the Ocean Zone in later seasons - a Titanic-style sunken ocean liner trapped within an air bubble on the ocean's floor.
 * Storm World is a juvenile SF series set on a world where the inhabitants (all sucked there through wormholes) are constantly at odds because of the scarcity of land, and above all fresh water.
 * Sea Quest DSV

Tabletop RPG

 * FASA Traveller module Rescue on Galatea. The main action takes place on the Ocean Planet Galatea.
 * Dungeons and Dragons module Q1 Queen of the Demonweb Pits. One of the alternate worlds accessible from Lolth's Web was the Ocean Planet "The Great Ocean". The human inhabitants "sail the ocean in great catamarans to carry the trade of their vast mercantile empire from island city to island city."
 * The Crowded Sea in the Al Qadim campaign setting (a subsetting of Forgotten Realms), explored in the Corsairs boxed set, serves this purpose.
 * Rifts World Book 7: Rifts Underseas - Pirates, Powered Armor-wearing Dolphins, Shapeshifting Orcas, giant squid Eldritch Abominations with tentacles miles long, fish-headed mutants, magic singing, playable Humpback Whales, floating cities, Extradimensional aquatic conquerors, and the U.S. Navy, among others. Actually pretty par for the course for Rifts.
 * Owing to the fact that the Elemental Pole of Water is located there, this tends to be the theme of any Exalted campaign set in the West. Common hazards include: Cannibalistic demon pirates, water and air elementals, ornery storm deities, aquatic variants of The Fair Folk, Magitek Lost Technology battleships (some of which may be sentient), gigantic sharks, crazed Wyld mutants, various tribes of aquatic Beastmen and the Lunars who rule them, malevolent empires of the dead...In fact, according to the Sidereals splatbook, the Convention of Water is the single most overworked group of Sidereals in existence. Considering that the job of the Sidereals is to keep Creation from going to pieces, this should tell you a lot about the West.
 * Fifty Fathoms is all about the swashbuckling piratey oceanpunk goodness.

Toys

 * Bionicle's Mahri Nui arc took place in an underwater setting, complete with Fish People, underwater vehicles and robots, a sunken city, Eldritch Abomination-like sea monsters, and vampiric squid.
 * LEGO Pirates was a more historical take on the trope, but still generic enough to qualify.

Video Games

 * The Legend of Zelda the Wind Waker, and its sequel Phantom Hourglass, mixed up the usual Zelda formula by changing its setting to an oceanic world.
 * Suikoden IV featured a setting like this, though it was set in an island country rather than a flooded world.
 * Mega Man Legends: "In a world covered by endless water..."
 * Skies of Arcadia is Pirate Punk and Sky Pirates with more emphasis on the former (at first). Characters travel between floating islands in flying 18th-century pirate ships (which later get upgraded to more modern-looking battleships). You play as a small band of pirates trying to take down the evil armada.
 * Sonic Rush Adventure is set on a cluster of islands where the main villains are robotic pirates.
 * The Aquanox series of futuristic After the End sub combat sims. Just think of it as "Sea Quest DSV meets Crimson Skies"...
 * Submarine Titans, which is basically Starcraft IN UNDERWATER !
 * Sleeper Xbox title Bloodwake is like this. The story suggests there's plenty happening on the game world's mainland, but since the protagonist is part of a pirate group who base themselves on islands and make a living preying on nearby shipping channels, all their warfare (and gameplay) is naval.
 * Dubloon
 * The Ocean Hunter.

Web Comics

 * In Homestuck, Post-Scratch Earth turns into this once Betty Crocker takes over and starts trying to Alterniaform it.

Western Animation

 * Pirates of Dark Water.
 * The Marvelous Misadventures of Flapjack .
 * Star Trek the Animated Series episode "The Ambergris Element" took place on the water world Argo.
 * Jabberjaw is set in a future where the ocean floor has been colonized.
 * Sealab 2020 and Sealab 2021.