Whenever the early Muslims became sick, they sought the advice of the Prophet (peace and blessings be upon him). It is related that when someone fell ill, the Prophet would recite one of these du'as for them.
Allahuma rabbi-nas adhhabal ba'sa, ashfi wa entashafi, la shifa' illa shifa'uka shifa' la yughadiru saqama.
Oh Allah! The Sustainer of Mankind! Remove the illness, cure the disease. You are the One Who cures. There is no cure except Your cure. Grant us a cure that leaves no illness.
Other duas: http://islam.about.com/od/prayer/qt/DuaSickness.htm