The Sage CRM Knowledgebase can be used effectively - it needs some tweaking though because, as you said, it can be a little clunky natively. For example, we have built a portal that allows customers (or consultants) to easily attach screenshots or other documents to a Case. You could do something similar with any CRM entity to make life easier.
As @WayneSchulz mentioned, good help desk software can be really expensive and most people will still want it integrated with their CRM system anyways.