Agility
- A customizable Issue and Bug tracking solution. It comes in both a Hosted model and a more traditional Enterprise model. [Commercial]
- http://www.agileedge.com

bugTracker
- Defect tracking solution written entirely in Java. [Open source, Apache-style license]
- http://bugtracker.sourceforge.net/bugtracker.html

BugRat
- A bug reporting and tracking system. [Open source]
- http://www.gjt.org/pkg/bugrat/

GRAN PM
- Java-based scalable and customizable bug tracking software. Supports workflow, PDF reports with charts, and multi-level security. By GRAN Ltd. [Commercial]
- http://www.granpm.com

Ozibug
- Web based bug tracking system, written entirely in Java and utilizing servlet technology. By Tortuga Technologies. [Shareware]
- http://www.ozibug.com/

WorkRoll Bug Tracker
- A web-based bug tracker, runs under any Servlets 2.2-compatible application server. No non-standard packages required; no database required. Installation, configuration, day-to-day administration, and general use are fully web-based.
- http://www.workroll.com/

TrackStudio
- Servlet-based issue tracking and project management software. Multi-level security, workflow, reports. [Shareware]
- http://www.trackstudio.com/

JIRA
- Innovative, browser-based J2EE defect tracking and issue management tool. By Atlassian Software Systems. [Shareware]
- http://www.atlassian.com/software/jira/

Scarab
- Servlet-based issue tracker - replacement for Bugzilla. [Open Source, BSD-like]
- http://scarab.tigris.org/

Bugzero
- Web-based bug/defect/issue/incident tracking software and change management system written in Java servlet (J2EE) and database technologies. By WEBsina. [Shareware]
- http://www.websina.com/bugzero/