Civil War Washington http://civilwardc.org/ examines the War in and around ther Nation's Capital from a variety of perspectives. Includes case studies on social, political, cultural and medical/scientific changes caused by the war.
Civil War Defenses of Washington http://www.nps.gov/cwdw/index.htm
Surrat House Museum http://www.surratt.org/
Ford's Theatre http://www.fordstheatre.org/ Contains links to many resources about the theatre, Lincoln and the War in Washington.