Military Tradition

At my late father’s funeral, The U.S. Marine Corp honor guard fired a 21 gun salute. Afterward, the commander placed 3 of the spent shell casings inside the folded burial flag that was presented to the family. What does each spent shell casing represent?

I don’t have an answer about the significance, but Cecil has addressed gun salutes here:
http://www.straightdope.com/mailbag/m21gun.html

Also, this cite points out that funeral volleys are not technically 21-gun salutes, which are reserved for Presidents and former Presidents:
http://www.mca-marines.org/Leatherneck/21gunarch.htm

The tradition of the gun salute is said to have come from when battles were stopped to clear the field of the dead, and the two sides would fire three volleys into the air when finished to signify that the deceased had been cared for. That carried over into three volleys over a casket at the funeral for the same reason. The three cartridge cases (usually, but sometimes one, and sometimes all of them) are to represent the three volleys for lasting proof and reminder that the deceased had received the proper honors and care.