AptOnCD is just a package archive backup tool with the ability to filter out duplicate packages to ensure minimal disk space usage. It is not much different from manually copying all the deb files in your /var/cache/apt/archives/ directory and does not backup anything else other than those cached packages.
If you are into creating a complete backup of your installation, you may want to read an excellent howto called 'How to backup your stuff UNIX-style
' in the Turials/Howtos section of the forums. In addition, you can also use SBackup -- although I strongly recommend you learn the manual method so that you will know what to do should things go severely amiss in such a way that restoring the backup from a Live CD environment becomes the only option.