as others post whenever this comes up, let me be the first in this thread to urge you to reconsider the "free" criterion and spend a little bit on what will be your billing and automation system for your company. ClientExec is my recommendation and it is affordable to begin with and they constantly have offers.
I agree completely with Plexi. Billing (along with support, uptime, etc) is one of the most important parts of a hosting business. I would also urge you to go ahead and save up some money and purchase a billing system such as WHM Autopilot or ClientExec. They are both easy to set up and integrate into your site.
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You won't find many good free billing managers really. Try doing a search using 'free billing managers' or other combinations, and see if that helps.
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A slight blow to your wallet is always worth it in the end, compared to what could happen if your free software falls over... These systems, that I and others have listed, also help you to look professional.