We also re-introduced the lyx LaTeX document processor that was cut from quantian 0.2, and added XEmacs which clusterKnoppix removes.
Packages which had been suggested but could not been added are gromacs (no native Debian package), giac (inofficial Debian package not quite up to packaging standards) and scipy (uninstallable, inofficial Debian package). As a general rule, official packages are clearly preferred.