Actually the company I work for released an open source billing option that's much like freshbooks. It's not feature complete yet, but the essentials are already there--you can create and send invoices, receive and post payments, and run a collection of reports. It's only going to get better from here on out.

You can play with the online demo or download, install, use it... without paying a thing--the beauty of open souce

I'm not sure of the rules about linkage here (I just got here and saw this post) but it's opensourcebilling dot org -- there's screenshots and links to the demo and download on the website.