Earlier, I posted a list of what I thought are worthwhile books dealing with the Civil War in the Indian Territory, but the war scarcely had an diminishing effect on the conflicts between whites and Indians elsewhere throughout the west. I've compiled a short list of titles, subdivided regionally.
The Deadliest Indian War in the West: The Snake Conflict, 1864-1868 by Gregory F. Michno.
All Quiet on the Yamhill: The Civil War in Oregon by Royal A. Bensell.
Shoshoni Frontier & Bear River Massacre by Brigham Madsen.
The Kit Carson Campaign: The Last Great Navajo War by Clifford E. Trafzer.
Navajo Roundup: Selected Correspondence of Kit Carson's Expedition Against the Navajo, 1863-1865 by Lawrence C. Kelly.
Battle At Sand Creek: The Military Perspective by Gregory F. Michno.
Sand Creek Massacre by Stan Hoig.
Finding Sand Creek: History, Archeology, And the 1864 Massacre Site by Jerome A. Green and Douglas D. Scott.
Confederate Pathway to the Pacific: Major Sherod Hunter and Arizona Territory, C.S.A by L. Boyd Finch.
One Blanket and Ten Days Rations: 1st Infantry New Mexico Volunteers in Arizona 1864-1866 by Charles and Jacqeline Meketa.
The Civil War in Arizona: The Story of the California Volunteers, 1861-1865 by Andrew E. Masich.
Nevada Military Place Names of the Indian Wars and Civil War by Daniel C.B. Rathbun.
Frontier Defense in the Civil War: Texas' Rangers and Rebels by David Paul Smith.
Minnesota and Dakota Territory:
The Dakota War: The United States Army Versus the Sioux, 1862-1865 by Micheal Clodfelter.
Over the Earth I Come: The Great Sioux Uprising of 1862 by Duane Schultz.
The Dakota War of 1862: Minnesota's Other Civil War by Kenneth Carley.
The Iowa Northern Border Brigade by Marshall McKusick.
Memories of the Battle of New Ulm: Personal Accounts of the Sioux Uprising. L. A. Fritsche's History of Brown County, Minnesota (1916) edited by Don Heinrich Tolzmann.
Memories of New Ulm by Rudolf Leonhart, edited by Don Heinrich Tolzmann.
Massacre Along the Medicine Road: A Social History of the Indian War of 1864 in Nebraska Territory by Ronald Becher. (also, an in interesting guidebook companion is Battlefields of Nebraska by Thomas Phillips).
Powder River Odyssey: Nelson Cole's Western Campaign of 1865 the Journals of Lyman G. Bennett and Other Eyewitness Accounts and Patrick Connor's War: The 1865 Powder River Indian Expedition by David E. Wagner.
Guarding The Overland Trails: The Eleventh Ohio Cavalry In The Civil War by Robert Huhn Jones.
The Indian War of 1864 by Eugene F. Ware.
Civil War in the Northwest: Nebraska, Wisconsin, Iowa, Minnesota, and the Dakotas. by Robert Huhn Jones.