I don't know what exactly solved this problem for me.
Of course I also downloaded the mp3plugin (don't forget that) from Sun/Oracle's website.
I also copied all the jmf and plugin jars to /Library/Java/Extensions/
And I ran jmfregistry manually and added the com.sun.media.codecaudio.mp3.JavaDecoder to the Plugins -> Codec tab
Still it didn't start.
But I noticed that I can start jmstudio.
So looking at the environment the jmstudio script sets up, I could manage to start id3v2 chapter tool:
sh -x jmf/bin/jmstudio
++ GetRealPath jmf/bin/jmstudio
++ pathName=jmf/bin/jmstudio
++ level=1
++ '[' -h jmf/bin/jmstudio ']'
++ echo jmf/bin/jmstudio
++ return 0
+ PROGPATH=jmf/bin/jmstudio
++ dirname jmf/bin/jmstudio
+ TMPDIR=jmf/bin
++ cd jmf/bin/..
++ /bin/pwd
+ JMFHOME=/Users/ngc/Downloads/chaptool-1.4.4/jmf
+ export JMFHOME
+ CLASSPATH=/Users/ngc/Downloads/chaptool-1.4.4/jmf/lib/jmf.jar:/Users/ngc/Downloads/chaptool-1.4.4/jmf/lib:/Users/ngc/Downloads/chaptool-1.4.4/jmf/lib/sound.jar:
+ export CLASSPATH
+ LD_LIBRARY_PATH=.:/usr/openwin/lib:/Users/ngc/Downloads/chaptool-1.4.4/jmf/lib:
+ export LD_LIBRARY_PATH
++ uname -r
+ UNAME=9.8.0
+ case $UNAME in
+ '[' 0 -gt 0 ']'
+ exec java JMStudio
I then used JMFHOME and CLASSPATH and added that to the ID3v2ChapterTool.sh