There have been plenty of Civil War bibliographies published over the years designed to assist the collector, librarian or researcher who is looking to assemble a first-rate Confederate library. At the top of the list are surely the venerable In Tall Cotton and its more recent cousin, In Taller Cotton. The granddaddy of all was Douglas Southall Freeman's South to Posterity: An Introduction to the Writing of Confederate History, published in 1939. A few years later came Travels in the Confederate States: A Bibliography by E. Merton Coulter.
The same cannot be said of Union bibliographies; at least until 1982 when Michael Mullins and Rowena Reed assembled The Union Bookshelf: A Selected Civil War Bibliography, which was published by Tom Broadfoot. Within the book's 81 sturdy pages, the authors have compiled and commented on the 246 books that they believed, at the time of its publication, represented the best work for those interested in studying or collecting books from the Union perspective. The book is divided into three sections: annotated works, regimental histories, and participant accounts. It includes an index and numerous reproductions of the books' title pages.
Though perhaps a bit dated, it is still a useful reference source for Civil War bibliophiles. I think it's still available from the publisher.