I have have been playing with Blinksale.com for invoicing recently. It is an online invoicing PO system that allows you to track invoices that are due, past due, and so forth. It also allows you to send thank-you's after a payment is made. It is designed to allow you to print an invoice that has been sent to you. You can set payment terms and repeat invoices automatically.

If you work in a very small nonprofit and are looking for a simple but powerful invoicing system, I would check it out. It is free to use lightly--3 invoices a month and has reasonable rates if you need to go beyond that.