If you are charging the same amount at recurring intervals, there are lots of options such as PaymentOnline.com and 2ndSite.com. However, if you want more flexibility, such as the option to bill some customers electronically and others on paper, you should check out BillingPros.com.

For billing out your time, or for billing recurring charges, I would recommend any/all of the following:

http://www.freshbooks.com
http://invoice.zoho.com
http://www.workingpoint.com

All are free or have free versions and allow you to send customized and professional-looking invoice. I prepare payroll for a handful of clients and they are charged a standard, monthly fee. These customers receive an invoice generated by Zoho Invoice every month, with no intervention or action from me. I also do virtual accounting work for some clients, but the number of hours are different every month. For these clients, I enter the number of hours into FreshBooks and send them an email invoice every month. Both services track the invoices sent and cue the customer to pay via check or PayPal (or whatever else you identify as acceptable payment methods).

HTH!
Deb

Source: http://www.freshbooks.com