You will need a working Debian Woody installation, including apt, and make sure the following packages are installed and working correctly.
If these packages are not installed, you can do so by typing
apt-get install packagename
Note: naturally you will need al dependencies too, but apt will take care of that automatically.
While writing this document, Woody only contains java 1.1, but for MMBase version 1.2 or higher is needed. I installed the packages from Blackdown. A list of Blackdown mirrors is at http://www.blackdown.org/java-linux/mirrors.html.
I added the following to my /etc/apt/sources.list , but the path might be different for different mirrors:
deb ftp://ftp.nluug.nl/pub/os/Linux/java/jdk/debian woody non-free
After that you can just type
apt-get install j2sdk1.3
Note: Although it must be possible to have more JRE's installed next to eachother, I wouldn't recommend it if it's not absolutely neccesary.