Naval Action, by Lou Coatney, is a set of free wargames rules for miniatures battles in the World War II Pacific Theatre. The page also provides some markers to use in place of model ships.
Rules: Naval
Battlefleet 1900 Pre-Dreadnought Naval Warfare: 1890-1905
The War Times Journal has a set of free Pre-Dreadnought Naval Warfare rules, designed for 1/3000 scale miniatures.
Archipelago of Gold
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 Naval Rules For Anglo Dutch Wars
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 WWII Era Battleship Rules
High Seas Drifter is a set of free wargames rules for playing battleship combats in the World War II era.