Knott just put up a wonderful multi-part post in the Barefoot Running thread, and she mentions bunions.

If you've had surgery, she suggests you might need very supportive shoes. Fit is everything, regardless. If you haven't had surgery, since you're just starting anyway, why not start running barefoot or, if they fit you, in Vibram Five Fingers? Nothing to un-learn and no having to do part of your run barefoot and part in shoes!