1862 is a set of American Civil War Campaign Rules designed for Johnny Reb, but which could be used with any miniatures rules set.
Then Holler is a new set of free wargames rules for game set in the American Civil War.
American Civil War is a set of rules for 25mm figures in a 1:25 scale.
Hardtack is a set of regimental Civil War rules based on the excellent Stargrunt II rules. With a scale of 1 fire = 3-5 men, it’s intended for fighting one regiment v another, filling the space between Johnny Reb and Brother v Brother.
The Jackson Gamers have a page with everything you need to know to start gaming Civil War Ironclads