I have used Kayako in the past and, while intensely pricey, it is great software. The KB in WHMCS is also great, though with fewer features, and comes at a much better price.
We use WHMCS and are very pleased. I don't see any reason to use an outside knowledgebase software when WHMCS already has a great one built inside, along with everything else you might need. I love Matt and his wonderful software!