I came across this interesting site which has as its goal to digitize EVERY document ever created by the Lincoln administration during the Civil War. They are a private company and receive no government funding. They started in 2002 and have quite a long way to go. If you go there, realize that some of the links are broken and they are very early in the process, so not a lot is there. Still, this is a very laudable project.
Best
Rob
http://www.lincolnarchives.us/