Pete Pellegrino has written a set of free miniature wargames rules called Damn The Torpedos. In the game, you customize your ironclad, and then take it out to fight in the Cvil War battle of Mobile Bay.
Pete Pellegrino offers a set of rules called Sink The Bismark! Pete writes:
Sink the Bismarck! is based upon the Battle of the Denmark Straits, May 1941. The game is designed to be played by a team or ‘Flag Staff’ determining the actions of each ship in their force. The Flag Staff can consist of any number of players; though recommend not more than 8 – 10 per staff. The staff must have one Admiral in charge of the staff and acting as commander of one ship, and a Flag Captain, commanding the second ship. The remainder of the staff is divided among three departments; the Navigation Department (NAV DEPT) responsible for ship movements, the Engineering Department (ENG DEPT) responsible for battle damage repairs and generating smoke screens, and the Operations Department (OPS DEPT) responsible for guns, torpedoes, and air operations. Each department executes its duties through the use of ‘action cards’ which they hold.
The rules also include downloads for paper ships, status sheets and card decks.
Matt Fritz offers a simple set of rules for recreating the 450 BC naval battle of Salamis between the Greeks and the Persians. The site even has links to paper models that you can use to play the game.