This evening I have been looking at with the KNOPPIX customization howto, and ran many of the interesting commands. I've setup a environment with Kalzium, OpenBabel, CDK, jython, PyMOL, and for development I included gcj and Eclipse. At some later point I will include kfilechemical too, but I want to make a deb package first.
Egon Willighagen (Fri,) studied this question.