Hi
The public API of Java3D has mostly remained unchanged from the version 1.5 to the version 1.6. The biggest difference is that Java3D 1.6 uses only the renderer based on JOGL 2 whereas Java3D 1.5 uses several renderers depending on the platform, including one based on JOGL 1. As a consequence, the installation has changed a bit, JOGL 2 is a lot easier to install and deploy than JOGL 1. I advise you to read this tutorial:
http://jogamp.org/wiki/index.php/Downloading_and_installing_Java3D