One of the things I've learned DMing all these years is that when you get into a seafaring campaign you're in for some extra work. I think next to psionics, one of the most extensively rewritten aspects of D&D is their sailing rules. In my research to bring ship rules to my Sea Princes campaign I've seen the whole spectrum of rules from no-frills to extreme simulation. I put all these in a hat and with a 3.5e campaign in mind, created a hybrid system of my own. This is some highlighted points of what I'm using:
Navigation: (Stormwrack) Three skill check fails and you're miserably lost. Maps or no maps.
Evasion of encounters: (Expert Set rule converted to 3.5) I like this simply elegant system for ship/monster chases. It's just an opposed skill roll modified by relative speeds. No messy chase systems that will take half the game session and the fact that encounters can be avoided speeds up sessions as well.
Movement rate and Wind Modifiers: (Stormwrack) This was lifted from the book. I saw no issues with it as it compared favorably with other editions. A typical caravel will make 30 miles a day average which is the exact length of a GH map hex.
Weather generation: (Stormwrack) Their chart was simplified enough that it still broke things down into cold, temperate and warm climates. Sure I'd love to use the official World of Greyhawk Weather Generator but its one of those uber-simulations that really slows the game down.
Damage from weather: (1e DMG with 3.5 conversion) This one I couldn't pass up. To create some quick random trouble on stormy voyages, now there are percentage chances for things to happen to the ship; from capsizing (there is a save for this one) to broken masts to crew falling overboard.
Repairing damage: (1e DMG) I went with an overall Hull Value system for ships instead of treating each damn section of the ship with HP like Stormwrack did. Consequently this makes damaging and repairing rules fast and low maintenance.
Grappling and Ramming: (Stormwrack/Expert Set) There were many ways to handle this and opposed skill rolls by the capatain seemed to fit the edition best. Ramming damage is the amped up version from the Expert Set as opposed to the feeble damage in Stormwrack that would have ships bouncing off each other.
Ship stats: (Stormwrack/Expert/1e DMG) For the most part I lifted these straight from Stormwrack including seaworthiness and ship-handling skill modifiers, cost and crew compliment. Their Hull Value and Armor Class I worked out from older sources. I changed greatship to galleon and I added the carrack by my own design to fill in a gap in ship size from caravel to galleon.
Ship weapons: (1e DMG/Stormwrack) This one is mainly derived from the siege weapon system in 1st edition with some tweaks by me that lead into my rules for handling fires. For instance, 10 flaming arrow hits do no hull damage but cause a roll on the burn chart where a Fireball spell explodes for .5 HV damage per die and a burn chart check per 5 dice.
Burn damage: (1e DMG/Expert Set) This hybrid system is a chart that is rolled on anytime an attack method causes a fire to spread. Depending on how high the roll is, the fire acts is staged in how much hull damage it causes each round. The five stages run from Minor to Critical in keeping with 3.5 names. Extra fires of a lower stage than the ship is currently burning do no extra damage but accumulate to raise it to the next stage. Then, in keeping with the Expert set, a simple system of 5 or more crew to reduce these fires a stage is used.
Encounters: (Stormwrack/Slavers/Drg #116) This one took a lot of time and is still a work in progress. I used 3.5 edition encounter rates, ship specific encounters from the High Seas article in Dragon #116, and I cobbled together several d100 encounter lists from varying sources. Notable is a sublist I gathered from various sources of Special Events. Sometimes an encounter isn't always a monster or ship. I came up with two d100 charts of various other sea-based events that could happen on a voyage. I can't wait!
I still have to playtest a lot of this stuff so I won't be publishing these rules, but maybe someday I'll refine them for public consumption. Comments and advice are welcome any time.