If you are running KNOPPIX install to HD, building custom kernel is pretty easy. If you mean a CD based KNOPPIX, it would mean a remastering that IMO is pretty cumbersome(every time Klaus comes out a new CD, the fork needs to follow, pain to maintain).

Since I use the poorman's install method, I adopt a 'middle of the road' approach as the following :

1. put the ISO file on the HD
2. put my custom kernel tree side by side on a ext2 loopback file under the same directory when the ISO goes
3. extra the boot.img(thus the miniroot.gz) and made modification to the initrc as well as copying the necessary modules to it
4. boot using my own kernel and at the end of initrc, mount my kernel tree to /lib/modules

In this way, I can keep up with the packages in KNOPPIX using my own kernel for as long as I want and I can switch kernel easily.

Of course it sticks to the machine but since the kernel tree is not too large, I believe about 15M compressed, I can put in on a CF(just use one that comes with my digital camera that is useless for that purpose) and I can still carry it around, together with KNOPPIX.

As for alternative knoppix kernel, my limited experience said that there is no such a thing. A kernel in linux means vmlinuz + ALL files under /lib/modules/`uname -r`(which got burnt into the CD) as a slight change in one of the function address exported by the kernel would make those modules unusable and how these address is in the kernel depends on what compilation option one choose when compiling it and what compiler used as well. So a standard linux kernel is actually 30M+(uncompressed) unless for special one where no module is used(like those special purpose router on a floppy stuff).

If Klaus can change his arrangement a bit by seperate out the kernel tree from the rest and use a similar approach as mine, it would be easier to 'inject' a custom kernel to KNOPPIX CD as all I need is to build another clooped kernel tree image and use knoppix-customize to replace that in the ISO.