is there some new innovative way around this problem specifically for SaaS/ web apps that charge businesses? (Ecommerce, consumer purchases, and virtual currencies are different beasts).

- Could we put together some type of invoicing system/coalition that lets users sign-up then pay by check? ie- you signup for a paid web service such as 37 signals/freshbooks/etc. Agree to pay by check. If payment isn't received within 15 days, the account is suspended. As a user, I'm pretty sure I wouldn't screw around with paying you since my data is important and continued access to the service. Businesses write checks all the time, especially for software purchases and services. This would pretty much eliminate the need for processing fees and all this crud. I don't know enough about ACH-debiting, but I believe there is no charge to do this. ie- you can do recurring payments on the bank account after one check is sent in.

Once again, this is only a suggestion for SaaS/business related apps.