This is not exactly about processing orders of shareware but an overall tool for business operations. This is software as a service that is called FreshBooks (freshbooks.com - formerly secondsite.biz)
I have converted my ISP business to using this system to create invoices and keep track of my receivables. This will allow you to invoice directly via email (or pay a little over a dollar to have them mail by USPS an invoice). It lets you know how your accounts are performing and how many are late. It has helped me have a much better handle on running my business. Further, the customer can log on and see what the status of their account is.
You can use Authorize.net or PayPal for processing credit cards with this system.
It will also do recurring billing for your montly subscriptions.
Where it may have application with regard to NB is that they have made an API that uses httpxml connections for updating and reporting. You can get data from in more ways than just from the web browser interface.
One might make a way to cause invoices to happen within an app!
David P.