In my experience it is wise to leave any knoppix specific packages. They're listed in their own section if you use Synaptic.

Yes a kicklist does need to be created initially but could then be used (with a bit of fine tuning) for later installs.

Most any application that you don't use can be nuked and apt will solve the dependencies. Just take your time and look at what will be removed. Synaptic makes it very easy to see what will be removed.

Of course it's not wise to remove x-windows.

apt-get remove libarts1 will nuke (nearly) all of KDE for example.