There are lots of Support Desk software. If you are already using WHMCS / clientExec you should prefer to use its inbuilt support system.
If you are about to select WHMCS or clientExec, you should not focus on its support feature. Rather you should focus on their features and find which one suits you best. New version of clientExec looks very modern and attracting.
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Oops, I see that Kayako is used at Rack911. I guess that you're not fond of it.
ArcticDesk is not being used by us, but may be considered in the future once the product is more mature. It's probably one of the nicer looking help desks out there and much more affordable than Kayako.
For me it's a client support solution that I'm looking for not really a hosting software thing.
Since this is a hosting forum, I can gain more insight by also asking about the inbuilt WHCMS and Clientexec support functionality of the software which I'm sure many already use.
What about the rate of support requests you expect per day? If you deal with very less number of tickets, you will find it less beneficial to buy a dedicated Helpdesk system and manage it. You may use built-in support module with your billing system. If you want to deal with larger number of tickets, you may consider Kayako, Zendesk, vision helpdesk, etc
We currently use the WHMCS built-in support system. It does fine, though it isn't our dream system (we have a Kayako license as well but years ago there were some issues with the integration and we haven't gone back to it since).
One thing WHMCS is lacking for us is its escalation system. We'd like a bit more fine grained control over tickets that can be escalated (the ability to escalate a ticket based on the sending email address).
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I guess that none of the free helpdesk software is worthwhile. I’m leaning towards an all in one solution like WHMCS or SPBAS like someone pointed out in another thread.
I know that individual tools are better than an all in one solution but I think that for many startups, solopreneurs and small businesses, all in one software is versatile and does the basic jobs needed.
If a business grows and is successful then one can upgrade to specific and customized software solutions.
I think the best option for starters would be the built-in helpdesk from WHMCS. It has "everything" like tickets, knowledgebase, unlimited agents etc. and all in one place, no need for customers to log in different sites. Why you should pay another licensed solution (and most saas charge per agent)?
You could also check the free php stuff out there like TrellisDesk, OsTicket etc.