Tony De Lyall offers a free Windows program to automate the American War of Independence miniatures rules written by Will McNally.
Elan Deluxe is a set of free rules for playing Napoleonic wargames. Once published professionally, it now is available online. This is a very well done, and interesting set of rules. The nominal scale is 1-50, with units representing battalions and regiments.
Bloody Big World War II Battles is a set of free wargames rules for large scale WWII battles. Each base in the game represents a battalion or regiment. The ground scale is either 3” or 6” to the kilometer. Time scale is 1turn = 2 or 1hrs. One model represents 30 or 10 vehicles / guns or half a battalion or company of infantry
Stout Hearts is a set of free wargames rules inspired by the classic Hal Foster Prince Valiant comics.
Generic Outlandishly Big Spacefleets (GOBS) is a set of free and easy-to-play rules for huge fleets of starships. The author writes:
G.O.B.S.! is fast-paced and easy to learn. Record-keeping is minimal; in most cases, ships blow up rather than retaining damage. (A two ship game of G.O.B.S.! would be over pretty quickly. This game is about fleets, Sparky! We want explosions all over the place!) The length of playing time is dependent on the size of your fleets, but an hour or two should do it for most cases. Wanna play longer? Build bigger fleets!