To make a .iso image from a directory of files, do something like this:

mkisofs -o /tmp/cd.iso /tmp/directory/

Note that to make an iso of a “DVD” directory that you want to be able to play in things like VLC you will need to do things slightly differently (and make sure that you have an appropriate VIDEO_TS directory in there).

mkisofs -dvd-video -o fredblonk.iso fredblonk/

If you break anything with the above, tough, it worked for me.