I have heard of such a system before, where you pay for diskspace, transfer, CPU time, and other resources by the cents (literally).
I believe the host was freebsdhosting.com. However, it seems to have gone out of business. A member of webhostingtalk.com also posted such a script (he might be from freebsdhosting.com) for free. Search the forum archive for it.
In my search for control panels i found a control panel that was designed for that very purpose though i cant remember where i seen it, all i remember was that is was for internal use with their accounts only, sorry.. if i come across it again though i will send it to you.