There are a million posts out there that cover how to make an ISO image of a CD/DVD. For some reason I was having a particularly hard time with a specific disk. It had long file names, funny folder structures and I kept getting all uppercase file names. I tried the stock dd if=/dev/cdrom of=~/[file-name].iso first and found that it was just not cutting it. The below seemed to work the best on multiple CDs and formats.

mkisofs -r -J -l -d -allow-multidot -allow-leading-dots -joliet-long -no-bak -o ~/[name-of-file-or-disk].iso /media/[source-folder]