I've used ClientExec for quite a while now. I've explored WHMCS as an option (because of the helpdesk feature) but I've stuck with CE as their support has been absolutely top notch and it keeps things simple for both myself and our clients.
clientexec. It takes up some time modifying the interface, signups..and such if you want to do more than just fill in the header and footer, but other than that, it's an excellent billing system.
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