One of the primary things we use JIRA for is the Kanban Board feature. We use it for managing our projects and issues as well as accountabilities within the company. We have a homegrown — I suppose you could call it a Six Sigma type — approach. We identify the six main projects and the six areas where you can make the biggest difference within the company. Then we identify six projects that we're going to work on within those areas.
We use the Kanban Board extensively. We use the Confluence facility on the backend. Really, we use Confluence and JIRA both together: Confluence for global planning and JIRA for issue and project management.