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.
The Civil War in 30 Minutes is a matrix game designed by Matt Fritz to help his students understand the American Civil War. If you haven’t looked into matrix games, you will find that they are useful in running meaningful campaigns.
The Battle for Henry Hill is a simulation of the First Battle of Bull Run designed by Matt Fritz for his students. The rules include an order of battle and links to paper figures.
Mike Willegal offers A Perfect Sheet of Flame, a set of free wargames rules for gaming the Amerian Civil War. Mike writes that this is the fourth version of his Iron Brigade system:
This forth version has a major revamping of the game mechanics. Gone is the sequential alternate movement system. In place is a order driven simatanious movement system. Orders must be generated by officers and isolated units may only execute their orders after a delay. Gone is the need for the results tables. In place of that, the player must perform some very simple math (adding up the sum a of a number of dice) followed by a simple divide. The result is intended to be a much more exciting, and fast moving game. The old system of tying morale to fire combat remains, though in an altered format. The overall effect of combat should be similar to the previous version, with a bit more luck thrown in. This should average out quite quickly in battle, as I have studied probilities of sum of a number of dice quite carefully in coming up with this system.
Rudi Geudens has written a modification of Richard Borg’s Battlecry game for miniatures. You need a set of the original rules to play, though.