You can read an extremely thorough article by the Library of Congress on the Care, Handling, and Storage of Photographs. This article also describes in detail all the factors that cause photographs to deteriorate. This article can be found at:
http://www.loc.gov/preserv/care/photolea.html.

• The Civil War Soldiers and Sailors System indexes approximately 5 million Civil War soldiers
• The War of the Rebellion: A Compilation of the Official Records of the Union and Confederate Armies
• Civil War Regimental Index from Dyer's Compendium
• Jefferson Davis Estate Papers online

• Civil War Burials Database Project
• Civil War Veterans Buried in Mexico City National Cemetery or the Corozal American Cemetery
• 

  Alabama

  • Alabama Civil War Service Database (surnames A - R

  Arkansas

  • Burial Places of Union and Confederate Soldiers in Arkansas by Edward G. Gerdes

  Colorado

  • Colorado Civil War Volunteers
  • Colorado Civil War Veterans (Grand Army of the Republic membership)
  • Colorado Civil War Casualties
  • Colorado State Veterans' Grave Registrations, 1862-1949

  Connecticut

  • Connecticut's Civil War and Spanish American War Pension Records
  • Connecticut's Deceased Veterans Discharge Files 1882-1936

  Delaware

  • Delaware Roster of Union Soldiers
  • Delaware's Union Colored Troops

  Florida

  • Florida Confederate Pension Applications
  • Florida Confederate Pension Application Files  
  • Complete Florida Confederate Pension Application Index PDF download

  Georgia

  • Georgia Civil War Pension Records
  • Civil War Resources at the Georgia Archives
  • Index to Georgia Confederate Pension Applications
  • Georgia Confederate Pension Applications
     

  Idaho

  • Idaho Civil War Veterans

  Illinois

  • Illinois Civil War Database
  • 1929 Illinois Roll of Honor
  • Illinois Civil War Rosters

  Indiana

  • Indiana State archives

  Iowa

  • Iowa in the Civil War

  Kansas

  • Kansas Civil War Veteran's Database
  • Kansas in the Civil War
  • Necrology of the Kansas State Grand Army of the Republic
  • Kansas State Military Databases

  Kentucky

  • Researching Your Kentucky Civil War Ancestors

  Louisiana

  • Louisiana Index

  Maryland

  • Maryland State Archives - Military Records Online
  • History and Roster of Maryland Volunteers War of 1861-1865 Vol. 1
  • History and Roster of Maryland Volunteers War of 1861-1865 Vol. 2

  Massachusetts

  • Massachusetts Civil War Research Center

  Minnesota

Mississippi

• The Jefferson Davis Estate Papers at the Mississippi Dept. of Archives and History

Missouri

• Missouri Men Who Served in Illinois Civil War Regiments
• Missouri's Union Provost Marshal Papers: 1861-1866
• Missouri Soldiers Database, War of 1812 - WWI
• Missouri's Union Provost Marshal Papers: 1861-1866

Nebraska

• Nebraska 1893 Census of Civil War Veterans
• Nebraska Civil War Veterans

New Hampshire

• New Hampshire Civil War Archives

New Jersey

• Record of Officers and Men of New Jersey in the Civil War 1861-1865

New York

• New York State Civil War Database

North Carolina

• NC Confederate Pension Application Request Form

Ohio

• Ohio Civil War Documents
• Links to Ohio Civil War Rosters
• Ohio State Archives - Civil War Searchable Databases

Oklahoma

• Index to Oklahoma Confederate Pension Records (pdf download)
   

Pennsylvania

• Pennsylvania Civil War Veterans' Card File Index 1861-1866
• Pennsylvania Military Index

Rhode Island

South Carolina

• South Carolina Confederate Pension Applications 1919-1926 (includes digital images)

Tennessee

• Tennessee Confederate Pension Applications
• Tennessee Southern Claims Commission Index 1871-1873 Claims for property taken by U.S. military personnel for use in the Civil War.
• Tennessee Confederate Soldiers Home Applications
• Tennessee Civil War Veterans' Questionnaires
• Tennessee Confederate Physicians

Texas

• Texas Confederate Pensions
• Index to Texas Confederate Pension Applications, 1899 - 1975
• Texas Confederate Indigent Families, 1863 - 1865
• Texas Adjutant General Service Records 1836-1935

Vermont

• Vermont in the Civil War includes rosters of Vermont units

Virginia

• Library of Virginia Online Military Records includes...
  • Confederate Disability Applications
  • Confederate Pension Rolls for Veterans and Widows
  • Robert E. Lee Camp Confederate Soldiers' Home Applications
  • Index to Virginia Confederate Rosters
  • Electronic Card Index to the Confederate Navy
  • Index to Confederate Veteran Magazine
  • Virginia Military Dead Database
• Virginia Confederate Pension Rolls-Vets & Widows
• Virginia Confederate Disability Applications & Receipts for artificial limbs
• Civil War Era Burials at Alexandria National Cemetery
• 1890 Veterans Census for Northern Virginia

West Virginia

• West Virginia Union Militia in the Civil War

Wisconsin

• Roster of Wisconsin Volunteers, War of the Rebellion, 1861-1865