Central Intelligence Agency
Cia: Intelligence in the Civil War [Pdf]
A multi-topic look at intelligence gathering, the tools used, and the people involved in both the North and the South during the Civil War. Comprehensive, interesting coverage from the CIA.
Other
West Virginia in the Civil War: The Jessie Scouts
A thorough discussion of the formation and use of the Jessie scouts who were mainly cavalrymen who gathered intelligence. Dressed as Confederate soldiers, they were used extensively by General Sheridan in the Shenandoah Campaign.
Other
Californians and the Military: John Charles Fremont and the Bear Flag Revolt
A brief retelling of John C. Fremont's expedition to California. Learn about his confrontation with Mexican authorities that led to the Bear Flag Revolt.
American Battlefield Trust
American Battlefield Trust: Civil War Biography: John C. Fremont
A profile of John Fremont makes note of his short stint as a the Union army officer.
Museum of the City of San Francisco
Virtual Museum of San Francisco: William T. Sherman and Early California History
From the memoirs of William Tecumseh Sherman you can read about his arrival in California during the Mexican War, his dealings with John Fremont, and the Bear Flag Revolt.