As promised, here are my naval combat rules. They're based on two principles:
1) D&D naval combat should be as D&D as possible, and
b) any rules subsystem should fill a single sheet of paper at most.
My basic rules take up less than half a page and could probably fit on a business card. I've filled up the page with optional rules: the nautical complications that Patrick O'Brien buffs will expect, from tacking against the wind to acting as ship's surgeon.
Ships have Armor Class. AC is the same as leather armor for peaceful/clumsy ships and chain mail for warships/maneuverable ships.
Ships have Hit Points. Most ships have 1 HP per minimum crew. Warships typically have 30 HP.
Ships have a speed. 30 feet/round (about 3 mph) is average. Ships have no maneuverability class or facing.
Ships have initiative. Ships have no initiative bonus. All crew and passengers act on the ship’s initiative.
Ships fire ranged weapons. Each round, a ship may fire one weapon per 10 max HP. Ballistae do 1d8 damage and catapults 1d10. Attack rolls are made as a level 1 fighter and have the same range as a shortbow. Every 10 passengers may fire 1 volley of arrows (1d6 ship damage).
Individuals can attack a ship. Divide individual damage by 10, rounding down. Ship weapons do x10 damage to individuals. The DM arbitrates non-damage spells. Ships save as a level 1 fighter.
Ships collide. Boarding follows normal D&D melee rules. A galley with a ram does 2d10 damage and may sail through a destroyed ship or back up from a whole one.
Crew die in battle. The crew takes one casualty for each HP of ship damage (half killed, half unconscious at 1 HP).
SAMPLE SHIPS: HP and speed vary +-50% based on ship quality.
boat: open boat, raft, keelboat. Spd 20. HP 3. AC as leather.
longship: Can land on shore. Spd 35. HP 10. AC as chain.
galley: heavy rowed ship. Spd 30. HP 30. AC as leather.
sailing ship: merchant ship. Spd 30. HP 20. AC as leather.
warship: armed sailing ship. Spd 35. HP 30. AC as chain.
leviathan: Absurdly large ship. Spd 25. HP 50+. AC as chain.
Technologically advanced ship: Stats as previous ship types, but AC as plate mail, d12 weapons, and/or speed +10.
And that's it for the basic rules! Everything further on this page is optional, to be used by the DM when the players start asking about advanced tactics: can we aim at their sails? Can we fire flaming arrows?
Crit Location: On a critical hit against a ship, the attacker may forego extra damage for one of the following:
1) Sail Damage: The ship' speed is slowed by 10 until the crew skips a turn for repairs.
2) Called Shot: The attack (non-critically) hits a specific character or object.
3) Weapon Hit: A ship weapon is destroyed.
Fire: If a flaming weapon crits, or an attacker fumbles a flaming weapon, or the ship rolls 1 on a save vs fire, the ship burns. It takes 1d6 damage on the opponent’s turn. On its turn, its crew has a 50% chance to put out the fire.
Wind Direction: Occasionally, strong winds affect navigation. Only rowed ships can go directly into strong wind. For instance, in a strong north wind, you can't sail north (but you can sail NW and NE).
Officer Actions: This rule is meant to involve multiple players on each turn. On the ship's initiative, a PC can use his/her turn to take an officer action. If you want important NPC ships to have skilled officers, add +1, +2 or +3 to the ship's AC, attack rolls, and damage rolls.
Captain: Order broadside: The captain's player chooses an enemy to attack this turn. Add the captain's Int or Cha bonus to the ship's damage rolls against that enemy. (Pre-Third Edition: Int bonus: 1/2 the number of bonus languages. Cha bonus: 1/4 max henchmen.)
Master Gunner: Aim weapons: The Master Gunner's player rolls the ship's weapon attacks, adding his or her Dex bonus (pre-3e: reaction bonus) to the attack rolls.
First Officer: Fill in: The first officer may take any officer action that is not being performed this turn.
Helmsman: Con the helm: The helmsman's player moves the ship. If the ship moves, add the helmsman's Dex bonus (pre-3e: AC bonus) to the ship's AC.
Ship Surgeon: Operate: Must have clerical/healing skill. The surgeon's player tracks damage to the ship. If the ship lost any HP last turn, the surgeon restores 1 ship HP.