As part of GSoC 2009, Egidijus Jankauskas has implemented a new version of the Growl notifications. This new version gets rid of the Java bindings and is implemented using a Java Native interface. It adds support for click on notifications (to get the focus on the window) and display of the buddy's icon in the notification. Furthermore, a library (growl4j.org) used in addition to the JNI allows to easily integrate this work in others Java programs.
I've commited this work into the trunk, let me know if you experience issues.
As a side note, Egidijus has also implemented a new way to select the popup message handler. The "best" one (i.e. the one that supports most of the features) is selected when available.
Congratulation and thanks again for your great work Egidijus!