I'm a fan of the Bugzilla bug tracking system that came out of the Mozilla web browser project. It is a web based system that makes it pretty easy to track issues with pretty much any piece of software. Furthermore, it isn't that hard to set up, so I have used it in more than one employment setting.
At work, we have a private Bugzilla installation that is only visible to employees. Given that everybody that can enter bugs should know how to fill in even the more complex fields, the enter bug form seemed a little inadequate. Our QA department really wanted to be able to specify the target milestone for a new bug to be for the next release when they entered a bug for a regression during the full quality assurance check a few days before a release.