Civil War Maps - Many Civil War maps from the Library of Congress.
HistoryChannel.com - Battles, biographies, chronologies, primary sources, and more.
The History Place - Timeline, battles, primary sources, and more.
A House Divided - Includes: Lincoln's America; the Slavery Debate; War, Politics, and Society; and the Aftermath. Well illustrated, and includes many primary source documents. Provided by the Chicago Historical Society and the Gilder Lehrman Institute.
The Valley of the Shadow - Primary source documents from the Civil War include letters and diaries from a northern and a southern community. Provided by the Virginai Center for Digital History and the University of Virginia Library.
Secession Era Editorials - Newspaper editorials on the Nebraska bill debates, Dred Scott, John Brown's Raid on Harper's Ferry, and the attack on Massachusett Senator Charles Sumner. Primary sources! Not an elegant site, but still useful.