Implement the AppIndicator for Unity systems. Since Ubuntu 13.04 there is no Vuze system tray anymore.
Since Ubuntu 13.04, support for other icons is lost, and apps must implement the AppIncidator to appear in the desktop. Guidelines are here: http://unity.ubuntu.com/projects/appindicators/
For what it’s worth, I filed a Feature Request with SWT/Eclipse about 2 years ago, and they suggested that someone knowledgeable in Ubuntu should contribute the change to SWT. See https://bugs.eclipse.org/bugs/show_bug.cgi?id=410217
It aint lost, just hard to find.