Fondly do we hope--fervently do we pray--that this mighty scourge of war may speedily pass away. Yet, if God wills that it continue, until all the wealth piled by the bond-man's two hundred and fifty years of unrequited toil shall be sunk, and until every drop of blood drawn with the lash, shall be paid by another drawn with the sword, as was said three thousand years ago, so still it must be said "the judgments of the Lord, are true and righteous altogether."
Abraham Lincoln in his Second Inaugural Address, March 4, 1865

The Official Records

The War of the Rebellion: The Official Records of the Union and Confederate Armies and Official Records of the Union and Confederate Navies in the War of the Rebellion can be found on-line at either of two excellent sites, each of which includes other useful resources:

  Cornell University's "Making of America Collection". This useful site also includes a number of other useful sources.

  eHistory.com. The same goes for this site as well.

Writings of Major Leaders

TeachingAmericanHistory.org Document Library of the Civil War Era. This collection includes writings and speeches of Abraham Lincoln, Stephen A. Douglas, Jefferson Davis, Alexander Stephens, William Lloyd Garrison, and others. 

Stonewall Jackson Papers

Horace Greeley Letter

Newspapers

  Cornell University's "Making of America Collection".  

  The Library of Congress Historic Newspapers Collection.

Brooklyn Daily Eagle, 1841-1902

Diaries and Letters

Soldiers, Sailors, and Marines

Union

Confederate

Home Front

Union

Confederate

Espionage

Rose O'Neal Greenhow Papers

Research Aids and Databases

The Civil War Archive File Index. Contains diaries and letters from both sides.

Northwest Ohio Civil War Newspaper Correspondence Index

National Union Catalog of Manuscript Collections

American Civil War Research Database (subscription required)

NewspaperArchive.com (subscription required)

Civil War Soldiers and Sailors System

Archives USA (subscription required)

National Archives Research Catalog

Repositories of Primary Sources 

Cornell University's "Making of America"

The University of Michigan's "Making of America"

Documenting the American South

U.S. GenWeb Project

Military Order of the Loyal Legion War Papers

U.S. Army Military History Institute

Schoff Civil War Collection

Auburn University Special Collections and Archives

University of Delaware Special Collections

Abraham Lincoln Papers at the Library of Congress

Informative Websites on Civil War Subjects

The Battle of Shiloh. The most comprehensive and informative site on the web relative to this important battle, sponsored by Civil War Gazette and the Center for the Study of the American Civil War.

Ken Jones' Eclectic Projects Page. This site contains links to many other Civil War websites.

U.S. Civil War Center

The Valley of the Shadow. Dual studies of Staunton, Virginia, and Chambersburg, Pennsylvania, during the Civil War.

The Ohio Historical Society's "Fight for the Colors" Ohio Battle Flag Collection. 

Music of the Civil War

Words and music of "The Battle Hymn of the Republic"

Words and music of "Rally Round the Flag"

Band Music of the Civil War in the Library of Congress

The Music of the American Civil War

More Civil War Music

Poetry and Music of the Civil War