We are making our choice between modernbill and WHMCS, but as i can see WHMCS is better when it comes to payment methods, but is it possible to use WHMCS and integrate Kayako support suit or support trio to use as a support instead of using WHMCS Support module?
With WHMCS, you don't need supporttrio or Kayako. Their support center can handle everything you throw at it. Yes, it's just growing, but it's a great operation so far, and I know of no other billing client with the capabilities for support that WHMCS has (except, maybe Ubersmith).
There was at one time a loginshare for WHMCS, but it doesn't work. i've seen it, tried it,and it doesn't work. The best answer is to use the built in support center, or, get creative and build your own . It's really not THAT hard to build a support desk (done it a time or three), and with WHMCS' template setup, it's incredibly easy to get it to work right.
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WHMCS does have a good support system built in. You could edit the files and put forms there and email it to your department, and use login share? Look at www.comparebilling.com and you can get a rough comparison.