The complete April 1865 Order of Battle for Appomattox Court House may be viewed here.
Separate listings available:
Army of the Potomac (Maj. Gen. George G. Meade)
Army of the Shenandoah (Maj. Gen. Phillip H. Sheridan)
Army of the James (Maj. Gen. Edward O. C. Ord)
Army of Northern Virginia (Gen. Robert E. Lee)