American Civil War Riverine Actions is a set of free wargames rules for ironclads, tin-clads, cotton-clads and all the fun and unique ships that plied the rivers of the United States during the ACW.
Rules: Naval
Death On The Seas Ancient Naval Rules
Death on the Seas is a set of free wargames rules for ancient naval warfare. Also, Death On The Seas ship appendix.
Bombs Away Carrier Game
Bombs Away is a simple, three page print-and-play game about carriers in the Pacific.
Naval Action
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.
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.