I have been using an online billing/accounting system since the first part of this year (2009). It has allowed me to move closer to my goal of utilizing the "cloud" for all my data including email, accounting, project collaboration and everything else. The service I have been using with great success is FreshBooks. It allows me to invoice my customers quickly and efficiently. It also allows my customers to view their invoices online.
FreshBooks has a neat feature that compares and rates your business with other businesses in the same category. My category is "Programming". They compare things such as average invoice amount, number of invoices, revenue from new clients and more. I was very satisfied to see that my rating was the highest you could achieve. Not sure what this actually says about my company except that I am doing really well compared to other FreshBook customers.
Here is my rating:

A couple other nice features I like and use:
- Estimates
- Time Tracking
- Emailing of Invoices and Estimates
- Expense tracking
- Allows others to bill me and automatically convert to expense
There are many more features. Click my rating if you would like to learn more about FreshBooks.
My Full report card:

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