We use Kayako for our support center and live chat for it.
It isn't really much about clients preferring it (at the end of the day they still get a ticket area, knowledge base etc). It is the features on the admin side that is lacking at WHMCS - things like SLA, billing capability, phone integration and a proper live chat system built into the helpdesk etc etc.
With Kayako, we can see clients ticket, chat and phone history in a ticket view. Makes it so much easier and that is just one example.
WHMCS is good to start with but if you want anything "extra" a separate helpdesk (with integration) is probably the best route.