I have been running the AF version of knoppix on a 128mb CF card, but I use it as an internal HD as it makes my laptop noiseless and the battery last longer as well.
However i guess you could do the same on a USB pen as long as the computer that you pluggin in it will support USB booting.
It would be like having AF2006 on a USB instead of the CD (you know that you can boot from AF2006 CD on any PC right?)

you can cut down AF2006 up to 100 MB if you only copy what you need. (or even lower if you have your own install of the AmigaOS)
then its only a matter of making the USB buttable.
I would use syslinux but other appllication like loadlin can work as well.
good luck
BiL0