I've used Jira, Confluence, and testing out FishEye. We use Crowd for single sign on stuff. I really like fisheye because we have tons of different projects on different repositories. Confluence is nice although it took some getting used to. Jira was awkward, but we're still running Jira 3 and we'll be upgrading soon. For what it's worth, Jira is the best issue tracking software I've used on the web.