Lowest priced online billing system?

The startup that I work at has built a Saas application that has around 20 customers so far. We make anywhere between $1000-3000 per customer depending on usage. We collect this revenue via check or bank wire, which reduces the number of fees we incur. We are in process of opening up the application to more users at a lower price point, but are not sure how to bill many people easily at an affordable rate. What is the lowest priced online billing that we can use?