You can use Java3d (1.4.0-beta3 Build 9 tested) with the blackdown j2re1.4 Ubuntu Package
Just download Java3d and install it into /usr/usr/lib/j2se/1.4/jre
If you want to use Java3d within Eclipse (Ubuntu Package available), just make sure that the blackdown jre is selected in the eclipse menu "Window/Preferences/Java/Installed JREs"
Get the Java3d source:
Have fun!