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/lib/j2se/1.4/jre (more detail above)
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
Download java3d-1_4_0_01-linux-i586.zip to a temporary directory, for example, "/tmp"
Unzip downloaded file
Unzip java3d-1_4_0_01-linux-i586.zip into "/tmp" as follows:
{{{cd /tmp unzip java3d-1_4_0_01-linux-i586.zip}}}
This will create a "java3d-1_4_0_01-linux-i586" subdirectory in /tmp where the downloaded files can be found. The file you need for manual installation is "j3d-140-linux-x86.zip".
Install Java 3D
Unzip Java 3D 1.4.0_01 into the "jre" directory of your JDK. For example, if your JDK is in "/usr/lib/j2se/1.4/jre", you would do the following:
{{{cd /usr/lib/j2se/1.4/jre sudo unzip /tmp/java3d-1_4_0_01-linux-i586/j3d-140-linux-x86.zip}}}
Verify that the j3d*.jar and vecmath.jar files end up in "/usr/lib/j2se/1.4/jre/lib/ext"
Have fun!