There was a lot of speculation about this issue on the POTC 3 thread a while back. Information from Wikipedia as well as interviews with the writers suggest that Will is freed from his duty as captain of the Flying Dutchman and can live out the rest of his life with Elizabeth and their son. Here is some info from the Wikipedia site.......
Although Will has been saved, and the Dutchman crew have regained their humanity, Will is now bound to being The Flying Dutchman's captain: he must spend ten years in the netherworld ferrying souls to the other side. Will and Elizabeth have one day together and consummate their marriage on an island before Will must leave. Will entrusts Elizabeth with the Dead Mans Chest containing his heart. Shortly after, Barbossa again commandeers the Black Pearl to search for the Fountain of Youth using Feng's chart, stranding Jack and Gibbs in Tortuga. Having anticipated Barbossas deception, Jack already removed the chart's center and sets sail in a small dinghy searching for immortality. In a post-credits scene set ten years later, Elizabeth and her son, William Turner III, stand atop a cliff overlooking the sea. A green flash heralds Will's return from the netherworld.
Filming finished on January 10, 2007 in Molokai,[16] and the first assembly cut was three hours.[17] Twenty minutes were removed, not including end credits, though producer Jerry Bruckheimer maintained that the long running time was needed to make the final battle work in terms of build-up.[18] A second unit shot at Niagara Falls.[19] One scene cut explained that if Calypso had greeted Davy Jones after his ten years of ferrying dead souls, then he would have been freed of his duty: in turn, Will is freed of his captaincy as Elizabeth remains faithful to him ten years later.[20]