You can run a ground wire to the first box that has the 3 wire in it, then connect all the ground wires together in this box so the ground is carried through to the following boxs. But, this ground wire that you install must go all the way back to your main panel and CANNOT be attached to a nearby water pipe or the water main. What route you take depends on where your main panel is located. If your main panel is on the outside of the house then you definatly want to run the ground wire protected by conduit. If in the basement then just run the ground through the floor and up into the wall.
Below is a link that further explains the requirements to change a 2 prong receptacle to to a 3 prong receptacle.
http://www.codecheck.com/250_50_commentary.html