The Civil War on the Web - The sites below have been recommended by scholars and librarians.
Abraham Lincoln: Impact and Legacy @ AmericanPresident.org (Miller Center of Public Affairs, University of Virginia)
American Memory (Library of Congress/ LOC)
Civil War Soldiers and Sailors System (National Park Service) -- Find information about individual soldiers, regiments, cemeteries, battles, prisoners, medal of honor winners, and national parks.
Civil War Women: Primary Sources on the Internet (Duke University Libraries)
Documenting the American South (University of North Carolina at Chapel Hill)
Valley of the Shadow: Two Communities in the American Civil War (Virginia Center for Digital History, University of Virginia.