If you have too many shots like that and don’t want to do it manually for all, let’s assume the dust wasn’t moving too much during the shoot. Instead of just cloning the dust away on the first photo, you duplicate the photo onto a new layer, clone out the dust on the upper layer and set the overlay mode to difference. Now you have the dust “filter”. Save that and apply it all your shots with the dodge overlay mode.
Update: Simon pointed me to a another wonderful commandline utility called Jpegpixi. It deals with another bad side effect of digital cameras, co called dead or hot pixels. Instead of using a difference map, it will allow to specify pixels or areas to interpolate. It will also only affect the jpeg blocks that require change and will not require the whole image to be reencoded.