I ran a 3e naval campaign, and here's the kind of things I researched the stuffing out of:
Watch Master & Commander. That totally shifted my view of naval operations and revealed how books like the seafarer's handbook were "off"
proper formulas for ship building. I researched a metric ton of real ship stats and came up with a formulas for how many masts, width, # of decks, draft based on the length of the ship.
They weren't complicated, but there is a general pattern in ship designs once you study actual ship dimensions. I could probably dredge up my spreadsheet that had the historical stats so I could discern a patter, and my simple ship stats spreadsheet.
Properly account for cannons, balista and catapults on a ship. Too many D&D sailing ships put 2 balista on the deck and call that a warship. Once the technology involves more modern (1700's) sailing ships, they were bigger and you could pack on the guns.
Rules for a party of PCs to contribute to the sailing and combat of a vessel. Basically, stuff to do when they aren't in hand-to-hand combat.
rules for calculating travel time to far away places (including adjustment for weather along the way)
sea monster attacks and resolution of ship to monster to character combat
ramming, broadsides, chasing, boarding rules
Marines!
Ship board life fluff and positions on a ship (that PCs might fill)
random encounters (monsters, other ships, weather, reefs, lost islands, fish schools, big fish (dolphins, whales), etc)
guidance for PC command hierarchy and inter-player behavior so the "Captain" isn't a jerk to his friends
Curses, superstitions, bad omens implemented as ACTUAL mechanics
Albatross!
Ship construction costs (so the PCs could run a ship construction yard or business)
Shipping and freight investment system (so the PCs can run or invest in the East India Trading company, etc)
Communication for ship to ship and for transport of messages from one land to another. One of the themes in my naval campaign was that humanity's ability to settle and colonize is limited to the acceptable delay time to communicate with others, so as to call for help or reinforce or resupply. I used magic to solve that problem (MEssage spell, etc). Without it, civilization won't spread farther than a few months distance for communication.
Just a few of the things I dealt with, and mostly had to invent because I didn't find a suitable nautical campaign source for D&D in the 3e era.
Oh yeah, support 3e!