1. Bluejackets and Contrabands: African Americans and the Union Navy by Barbara Brooks Tomblin (Univ. Press of Kentucky, 2009).
Tomblin's study examines the symbiotic relationship between the U.S. Navy and black southerners along the Atlantic seaboard. Slaves were freed by the thousands and makeshift colonies established through coastal raids and occupation. In turn, the navy received knowledgeable spies, guides, and pilots. I'm not entirely sure, but I believe this is the first book length treatment of the subject.
2. The Beat of the Drum: The History, People, & Events of Drum Barracks Wilmington, California by Don McDowell (Graphic Publications, 1993).
Just glancing through it quickly, McDowell's Drum Barracks (Camp Drum) study looks like it contains some worthwhile passages for students of the Civil War in the Far West. There's information about the post itself, some nice maps & illustrations, short biographies, and a brief California Column history.
3. The American Civil War in the Indian Territory by John Spencer (Osprey, 2006).
On the face of it, the book looks like a reasonable introduction (with an emphasis on the war's later years). The artwork created for Osprey books has certainly improved in recent years.