Archipelago of Gold is a set of free wargames rules for use with the constructable, collectable Pirates of the Spanish Main ships from WizKids. From the BGG description:
These rules use the Pirates of the Spanish Main and a hex map to allow you to explore wild islands for gold, build large fleets, settlements, cities, forts, and train your crews to become superior gun crews. Get more gold back to your settlement, and you can build more than your opponents.
1666 is a set of free wargames rules for naval combat in the Anglo Dutch wars. The game is designed for 1/2400 ships on a 2 inch hex grid. Direct download.
High Seas Drifter is a set of free wargames rules for playing battleship combats in the World War II era.
Pastor Mueller offers a set of Fast Play Trireme Rules
Steel Ships and Iron Hearts is a set of free wargames rules for pre-dreadnought naval combat. The rules set dates to 1982 and was played by the Olympic Wargaming league. Classic stuff.