National Archives and Records Administration (NARA)
Government agency responsible for managing records of the federal government.
Various historical records, including now-public Census data, and images.
University Publications of America Their guides point to a lot of original material, not just on the
Civil War. You would need to find libraries with that material though.
H-CIVWAR - a discussion group on teaching about the Civil War.
I had some problems with this site but they should be fixing it.