The Kayako Helpdesk is very helpful if you have multiple staff and a heavy ticket volume.
We've been using WHMCS for a number of years. Our daily shifts have 8-10 staff online during the day. WHMCS really hasn't had any issues with us.
While we use Kayako for our Live Chat, we are currently still using WHMCS as the ticket system. We were contemplating a swap over to the Kayako helpdesk (we had used it back in 2005 when we first purchased the software), but as of yet we haven't made the move again. The helpdesk, when we used it before, was just overkill for our needs (and we used to get about 50 tickets per day and had 5 staff online at all times).
Kayako is powerful - it's sometimes TOO powerful for a small operation. WHMCS hasn't had any issues for us.
I see that the license we purchased back in 2005 now retails for $17,899 (now called Fusion w/ Unlimited staff). I can tell you without a doubt, if I was to purchase it today, I wouldn't be spending that much money on it! That's some of the joys of getting in with companies when they're first starting up. I want to say when we purchased the license it was less than $400 back then.