ITracker is a Java J2EE issue tracking system designed to support multiple projects with independent user bases. It supports features such as multiple versions and project components, detailed histories, per project user permissions and multiple email notifications.
Here is a semi complete feature list for ITracker:

System:
J2EE 1.3 Application
Utilizes Jakarta Struts
Platform independent
Database independent
Pluggable Authentication -- Coming in 2.2

User:
Ability to create issues
Ability to edit issues
Attachment support
Detailed histories
Email notifications
Full issue activity auditing
Issue searching
Optional auto-login
Per project components and versions
Per project custom fields (String, Integer, Date, Lists) -- Coming in 2.2
User preferences psdk03

Admin:
Attachment management
Customizable via resource bundles
Full i18n support
Optional self-registration and forgot password features
Project locking (complete, view only)
Project level options
User level per project permissions
User locking

Reporting:
Severity report
Average completion time report
Issue export to XML or CSV
Ability to add new reports

Clients:
Web client (Full Featured)
Eclipse Plugin (View Issues only)
Web Services API (View Issues only)