Good post Stephen! I do not have Knoppix installed on my harddrive (I boot from CD on my laptop) - but I do have SuSE as the primary operating system on my desktop.

The procedure that worked for me was:
Boot from rescue CD
Make sure my Linux partition is not mounted (umount /dev/hdb2)

My partition is reiserfs, so the following command checks the partition:
reiserfsck --check /dev/hdb2

I repaired it with the followig command:
reiserfsck --fix-fixable /dev/hdb2

Cuddles - I saw you used to support Win98. Sounds like an interesting thing, but probably stressfull. Anyway - a good reference book for Linux is "Running Linux". It can help a lot.