Ancestry.com has a collection entitled:

Civil War Prisoner of War Records, 1861-1865, found at:

http://search.ancestry.com/search/db.aspx?dbid=1124

I have not used it so cannot validate it's usefulness.

See also:

http://www.google.com/search?client=safari&rls=en&q=civil+war+prisoner+of+war+records&ie=UTF-8&oe=UTF-8