Pikette Squared is a set of free wargames rules for playing games set in the late medieval and renaissance period.
David Heading offers a set of free wargames rules for Renaissance Naval Battles.
The Armchair General writes:
A GLORIOUS VICTORY (AGV) is a reasonably quick and easy set of wargames rules designed for the period of warfare from around the early 15th century through to the latter part of the 16th century, thus covering the War of the Roses and most of the Renaissance period.
Barded Fury is a set of early Renaissance rules from the Ambler Gamers. You can get them from their Yahoo Group.
The Junior General offers a set of rules — and paper ships — for the 1571 battle of Lepanto.