I have flat feet and have found the best answer to be orthotics, and believe it or not, the least expensive ones. WalkFit can be purchased at Target or BB&B. Even if you don't have flat feet, it keeps your foot honest when you are putting lots of pressure on it.

Another thing that VASTLY improved my foot health as it applies to cycling is the Yoga stretch where you start squatting like a catcher,then move your body into an arc, like an upside-down boomerang, hands in front. Slowly walk your hands closer to your feet, keeping your feet as flat on the ground as you can. Stretching that plantar fascia on the bottom of your foot will help, as it is attached to the ball of your foot (as well as your heel).