Besides the Digital U.S. Congressional Serial set's treasury of War and Navy Dept. reports, the Official Records of the War of the Rebellion (OR) are essential primary sources for Civil War research. These contain after action battle reports and other tremendously important documents and are broken up into two sections for army and navy operations. Online access provided by Cornell University's Digital Library.
National Park Service Civil War Sesquicentennial
Naval History & Heritage Command
Official Records of the War of the Rebellion: Army HIKS Repository W 45.5
Official Records of the War of the Rebellion: Navy HIKS Repository N 16.6
United States Provost Marshall (Provides information on military enrollment, desertions, and official policy documents.)