Where I was able to mention earlier that JChemPaint now runs with free (as in open source) Java virtual machines, I just tried to run the core Jmol renderer, using the Integration.java which comes as an example.

Sadly, the original screenshots got lost there were made with jamvm 1.3.3 and classpath 0.19.

It is very slow, however. I have not tried it with other free virtual machines, which are supposedly faster. It is a good start nevertheless: it means that a Jmol based Bioclipse plugin will work with free virtual machines too.