When creating an ext3 filesystem with Knoppix 3.1 the filesystem is created with an extra option that prevents debian woody from being able to fsck it correctly (hence it cannot boot). Too get around this after you have created your ext3 filesystem (mke2fs -j <device>) execute the following commands
debugfs -w <device> feature -dir_index Ctrl-D
Debian Woody should now be able to use the filesystem without problems.
There are notes on remastering knoppix at http://www.knoppix.net/docs/index.php/KnoppixRemasteringHowto. This will let you create your own, custom, knoppix based distribution
One page links to KnoppixNotes: