Unless you want to sale premium support you would surely settle for the free inbuild WHMCS version. Definitely lucks a few things but works perfectly well for most support tasks.
Figured I would also add SupportPal (formerly ArcticDesk) to this thread. SP is built by the folks behind LicensePal and seems to be a great cheap product.
It appears to be more of a Kayako 3 type product in terms of feature set so not as advanced but at the same time not significantly cheaper than Kayako 4.
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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.
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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
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I prefer to use WHMCS system, the user only need to log in to one system for billing and support. Customers don't like to have to log in on 2 different systems.