I haven't been able to get this idea out of my head. I floated the idea past a couple of players, and it's an idea that grabs people. I've been scratching out some notes here and there, looking through some old books... the usual.
The Black Sun Trading Company. This is an idea I have, where a consortium of Lawful underdark races form something like the Dutch East India Company. There are a fair number of really nasty lawful evil types down there, most of whom are pretty xenophobic, and in an environment like the Sunless Sea where they have to associate their lawful nature relies on a rigid set of codes governing how trade will take place and how tariffs will be paid. This naturally gives rise to the smuggling and piracy operations of the less lawfully inclined. A short list of the Lawfuls includes Aboleths, Beholders, Duegar, Illithid, Hobgoblins, Rakshasas, Fire Giants, Medusa, Dark Nagas, Xill, Neogi, Sahaguin and maybe Wights. For Chaotics, you have Derro, Yuan-ti, Orcs, and Ghouls. Neutrals include Drow, Goblins, Kuo-toa, Lizardmen and Stone Giants. (Grimlocks, Quaggoths, trolls and the like I plan to use in the role of savages, whereas most of the humanoids listed above will be labor for the brainier races.) Also, if anybody has a suggestion for a better name than Black Sun, I'll take it.
The Seven Seas. I don't have seven, but the idea is for multiple complexes. The Sunless Sea is most likely the largest. The Darksea (Dungeoneer's Survival Guide) is another one. Most of these will be other areas that will be discovered in play, so I haven't really be worrying about the names just yet.
The Underdeep. These are caverns where the Sunless Sea is bottomless. Still black water of seemingly infinte depth. Who knows what horrors lie in dreamless sleep in the endless murk. (I have to work in some HPL here. I just do.)
Portals. There are caverns down there where the bonds between this world and the next are strong. Careless wanderers could end up in the Lower Planes, drifting on the River Styx or perhaps into Abysm or Porphatys (sp?). I'm not sure how closely I'll stick to D&D cosmology, but I like the idea of sailing into the Underworld. I also like the idea of basing different areas of the Sunless Sea on different cultures' underworlds (like the Aztec's Mictlan.)
Hellspike Prison. I have no idea what this is, but I liked the name so I nicked it. I'm planning on using it as the prison from the opening of Dead Man's Chest, except it's a contract prison staffed by Beholders, and a wholly owned subsidiary of the Black Sun Trading Company.
Skartaris and Pellucidar. Hollow World enthusiasts will recognize these. Probably pretty distant from the Sunless Sea, this would be the repository for underground pulp material. Unyielding sun orbs, jungle, dinosaurs, tribes of savage women, superintelligent apes, the usual stuff.
Muspelheim. The City of Fire Giants. These guys have pioneered blackpowder cannon technology. I know I like fire giants, and I know I want cannons, but that's all I have planned here so far.
Skullport. I'll be nicking this pretty much wholesale. And, since a lot of the underdark ships will be retrofitted surface craft, Skullport makes a good import point between the underdark and the surface oceans. (At least, I remember them connecting, though its been years since I've read FR. Suffice to say if Skullport didn't link the surface sea to the underdark, it does now.) This is in addition to locally constructed watercraft like Duegar ironclads and Illithid Nautiloids. (I've been looking through a lot of old Spelljammer stuff for alien ship designs. The mind flayer stuff is pretty dead on what I'm looking for, the other races are hit and miss.)
Kidnapping. In addition to surface craft, surface sailors are going to be in a valuable resource. Sailing in the underdark is a relatively new idea and its in a boom, so specialists are in high demand. Spellcasters dealing with Wind in particular; they're useful to a surface craft-- on the Sunless Sea, they're rock stars. (Perhaps enslaved rock stars, but rock stars nonetheless.)
That's what I have so far in the broad strokes. I'll probably be working in a lot of AE stuff as I go along as well. (Chorrim, Slassan, Harrids, Inchon, Shadow and Blade Trolls, and so on.) Further updates as events warrant.