The Battle of Chaeronea (338 BC) featured the Macedonians under Philip against a combined force from Athens and Thebes. The Junior General has rules and paper figures at the links.
Rules Link
Paper Wargames Figures: Link
Miniatures Rules
Schlachtfield Ancients
Schlachtfield is less a set of free wargames rules than a series of thoughts about ancients wargames. It is interesting nonetheless.
Beer and Pretzels Modern Micro Armor
GHQ has a free pdf of its Beer and Pretzels Modern Micro Armor game, formerly a commercial effort, now a set of free wargames rules.
Trireme Game Rules
The Trireme Battles blog offers a set of free wargames rules for trireme battles.
Beer and Pretzels WWII Micro Armor
GHQ has a pdf of its Beer and Pretzels WWII Micro Armor, originally a commerial set, now a set of free wargames rules.