I would have to say that modernbill & clientexec are the best out there. Im speaking from a couple years experince. I have used alot of 3rd party software and for the price I would have to go with clientexec. They just release a new version and it has alot of nice features. If you'd like to test it out I can provide you with a license for $10/mo. Modernbill though is also very nice but it costs more, and can be kinda confusing.
Would have said whmcs, when i purchased it the script was great, support was fantastic, and not many people used it. Although now, its a good script, too many people use it as the script can be licenced and there are tonnes of resellers and the support is ok, though not friendly.
Clientexec has a horrible loading time for the order system, which could scare of some potential customers. Clientexec is very secure for the price, but that is also with modernbill. Check out mblicenses.com, they offer 50 clients for $13.95/mo, and when we upgraded they were very quick in doing so.
I am currently using WHMautopilot and I like it. It is very easy to use.
Modernbill I have heard good things about it too, but some folks are complaining that it is not easy too use.