It would be outstanding if there was a back end system like Mailware or Mail order Manager. I have used them with other shopping carts and they help streamline the whole process. Short of an entire back end system like the ones I mentioned, it would be nice if this would create purchase orders for items that were not in stock and then when the items are received into stock it brought up the orders that were waiting for the items letting us know they are ready to fill.
You might look into http://www.ez-om.com if you are used to using a back-end order management system. It support PO's to drop-shippers, but it doesn't do notification of “back in stock”. The order simply remains visible in what's called the order queue (like a manufacturing work-in-process queue).