La Felissima Armada is a set of free wargames rules for naval skirmishes between England and Spain in the Elizabethan Age.
Periplus is a free two player wargame that abstracts a battle between two fleets of ancient greek warships.
The Junior General offers a set of rules — and paper ships — for the 1571 battle of Lepanto.
Seas of Lead is a set of free wargames rules for World War II Naval games. Along with the rules are some good looking unit data cards that they made using the Magic Set Editor.
Here’s a set of very simple WWII Naval Rules.