The links between the help desk and Jira issues and between Confluence and Jira issues are most valuable. I can write requirements in Confluence and link them to user stories in Jira and test cases. I can see my test coverage and all that kind of stuff. The integration between these three is very useful.
It is pretty customizable, and it integrates well. There are a lot of add-ins and a lot of connectors to third-party products. In my last company, we used Test Royal for managing all the tests, and it integrated perfectly with that. For any issue or bug, we could see what tests have been run and the complete history of the tests.