We really like HostBill, as it integrates all of your automation, with a very good ticket system and live chat. Live chat and ticket system has macros (pre-written answers for common questions) and the ability to link a knowledge base (also included) article.
While the 'best' anything is going to be subjective (personal preference), selecting a helpdesk that's continually buggy and continues to stall development is not really the wisest choice for the 'best option'.
I do agree that WHMCS needs some helpdesk work, however it's getting there, especially with improvements made in 6.3
Tom Whiting, WHMCS Guru extraordinaire
Linux problems? WHMCS Problems? Give me a shout
Check out my WHMCS Addons
+1 - 866-546-8914 / skype - admin_139201 / twitter/facebook - @whmcsguru