I just wanted to give a shout-out to the members of the jTrac project. jTrac is an issue-tracking system which can be installed out of the box as a stand-alone server using Jetty and HSQLDB, or can be installed as a war in an existing server.
jTrac was very easy to install in our existing JBoss instance and required only a few settings and a directory for storing attachments and the application's HSQLDB database files. Once you have it installed and configured, you can create spaces for each of your applications. Each of these spaces can have a set of custom fields as well as a custom set of states and transitions. Write access to each space is limited to only members of that space. In addition you can make transistions dependent on a particular user role within the space.
The application seems to be mature enough to be feature complete, but does still have some minor nice-to-haves (book-markable searches, Eclipse Mylyn integration) and missing ui polish.