This post is really only a placeholder for the result: I managed to create a bootable ISO file from the Windows Server 2003 installation disk, but it has been nothing short of an ordeal to get to this point. I will try to record my adventures at a later time, using the notes below (which you can ignore for the time being).

Nero Express will only take a boot image from a floppy drive, ISO buster can extract everything and then some, but can't create bootable images, mkisofs should be able to, but consistenly fails to respond to what I believe to be a corect command line, MagicISO would probably work painlessly if it would not be crippled to less than 300MB. Undisker did the trick, even though it claimed errors at the beginning of the process.