Chickamauga and other Civil war Stories ed. Shelby Foote )the Foote fans here should like it)
Civil War Fantastic ed Martin Greenberg
The Fantastic Civil War ed. Frank McSherry
Confederacy of the Dead ed. Gilliam, Greenberg, and Kramer
Like the 3 preceding, these two books will appeal to the fan of horror/SF as much as the civil war aficiando :
Bring the Jubilee Ward Moore
The Guns of the South by Harry Turtledove
Both are set in an alternate universe where the south won the civil war. The Turtledove book has at least one sequel.
The best civil war short story I've read to date was published in Year's Best Fantasy and Hotrror : Seventh Annual Collection ed Ellen Datlow and Terri Windling, pub 1993. It's called "The Sunday-Go-To-Meeting Jaw", and it's by Nancy Collins. The story deals with the return of a maimed Confederate veteran (thought long dead) to his wife and children. It's heartbreaking, beautiful, and a good depiction of life in Arkansas after the war. The ending is one of the most gutwrenchimg things I've ever read. I've run across this story in several anthologies , and I recommend it highly to anyone.