Here is the official Library of Congress site of Selected Civil War Photographs. The site contains 1,118 photographs. Most of the images were made under the supervision of Mathew B. Brady, and include scenes of military personnel, preparations for battle, and battle after-effects. The collection also includes portraits of both Confederate and Union officers, and a selection of enlisted men.
The nice thing about this site is that it is chronological and you can view the photos in larger format and sometimes in higher resolution then on some other sites.