We recently switched to modernbill (aka PleskBilling). I've used several systems, and modernbill seems to be the most advanced, although complicated system. Honestly, their support is pretty much useless, and Ive found several small bugs in the system (purely UI bugs, nothing really as far as billing itself goes), but I still favor it over WHMAutoPilot.

However, Ive heard many good things about WHMCS. I would look into that one. The only reason we didnt use it is because there seems to be a little more control with modernbill's pricing config.