I've found several of my own ancestors in the Fold3 Civil War Collection.
Here is the info straight from them:
Access the Civil War Collection
To remember the commencement of the Civil War in April 1861, Fold3 invites you to explore all records in its Civil War Collection for free April 14–30.
Explore Civil War documents featuring everything from military records to personal accounts and historic writings. Soldier records include service records, pension index cards, “Widows’ Pension” files, Navy survivors certificates, Army registers, and much more. Other record types include photographs, original war maps, court investigations, slave records, and beyond. Items such as the Lincoln Assassination Papers, Sultana Disaster documents, letters to the Adjutant General and Commission Branch, and the 1860 census are also contained in the Civil War Collection.
Confederate-specific records include Confederate service records, amnesty papers, casualty reports, and citizens files, as well as Confederate Navy subject files and Southern Claims Commission documents.
Join Fold3 in its commemoration of the Civil War. Discover information on famous participants as well as your own Civil War ancestors through documents, photos, and images that capture the experiences and vital information of those involved in America’s deadliest conflict. Then commemorate your ancestors by creating or expanding memorial pages for them on Fold3’s Honor Wall. Get started searching the Civil War Collection here.