Ooh, nice. It makes my dungeon building bits tingle.
First thing I can think of is a room that the heroes get locked in and then fills up with water. An undead or giant octopus in the room is pretty much a given. It's a classic. Or cliche depending on your feelings. It could be either a deliberate trap or just something that happens.
Ghost Pirates! Sorry but I had to say it.
Strangle-weed. Use stats for a Strangle Vine (er, Fiend Folio maybe?) Some random patches but some patches cultivated in strategic spots by the pirates (and other inhabitants.)
Giant crabs scuttling through the sargasso like weed that infests the area. (I've just assumed a sargasso like setting with ships of the ages trapped in it. Sorry if I've assumed too much.)
A heroic duel in the rotting rigging far above the rotting deck of old man-o-war. Is there an NPC who has a particular mean on for one of your PCs? S/he provokes the PC (something like shoot at them, missing or slightly wounding) then flees into the rigging. Shooting at him proves useless as the old shrouds and lines give him too much cover. Keep the rest of the heroes busy with mooks. Someone has to go up into the rigging to get the bad guy or else s/he can just keep sniping.
Lost treasure in a hidden bulkhead. During a fight a PC or villain gets knocked through the bulkhead and lands in a pile of doubloons. Then the ship starts to sink/collapse. How much loot can the heroes get out before the whole thing goes down to a watery grave? If there's still villains alive they're trying to snatch as much loot as they can too.
Merfolk who hate the pirates (the lonely pirates steal their women folk) live in lowest parts of the graveyard. If the heroes are careful and respectful they could win the merfolk over to their cause. There's a group of young hot heads who hate 'dirty leggers' but who can be won over, intially by the idea of killing 'leggers' but eventually they come to like and trust the heroes.
Underwater passages that need to be swum through and that have many hazards to snare and catch the unwary. And of course they're pitch black. How available is magic light? And some are the haunt of horrible things: aquatic Dark Mantles, Ghouls. Nothing too dangerous unless your heroes have some sort of water breathing abilities.
A cell with kidnapped wizards. They are wary of the heroes because of the illegal nature of their studies.
A cell with kidnapped mermaids. They distrust all 'leggers' and can only be won over by other merfolk.
Speaking of ships of the ages: at least one of them has to be inhabited by some sort of vampire, lich, what not. This powerful, terrible being has lived here for centuries uncounted and knows many dread secrets. It tolerates the pirates because their leader has bribed it. Some money but mostly with sacrifices and more secrets. It's not implacably hostile to the heroes. It can be won over by promises of knowledge, magical knowledge being the most prized. If it can't be won over, well, it does have an eternal hunger for human blood/souls/brains.
Sea Serpents! How have I got this far and not thought of Sea Serpents? The environment provides ideal spawning grounds for the bad tempered, toothy beasts. The heroes stumble upon a nest of serpents, complete with eggs. Human remains are scattered through the lair with just enough shiny stuff to lure the greedy. Or, if your heroes are not that greedy, one of them falls through a rotting piece of deck and lands in the middle of the nest of sleeping serpents. Hilarity ensues.
Ropes to swing from. Maybe from one rotting hulk to another, just in time to prevent the BBEG sacrificing the beautiful princess/prince.
A great cabin is being used by the pirates. It is just above water level. It has a large hole in the floor. The pirates keep sharks nearby by dumping offal and such forth into the water through the hole. When the heroes attack they try to knock them into the water.
That's about all for now. But if I get any more ideas I'll pop back in and write them up.
cheers and have fun!
