You'll have to violate the iso9660 standards but it is necessary if you want to preserve your filesystem and filenames and shouldn't be an issue as long as you are using a modern OS like Linux.
genisoimage -o Backup-Myfiles.iso -r -J -joliet-long /some/path/
You will get errors like below (even enabling joliet-long didn't help)
genisoimage: Error: /some/filename.pdf have the same Joliet name
Joliet tree sort failed. The -joliet-lo........
genisoimage: Directories too deep for 'Backup/My Documents/My Music/iTunes/Album Artwork/Local/5928CE9C1AFAC465/07/15' (7) max is 6.
Some people said choosing the --iso-level-4 option will help. I just opted to add the "-D" switch and everything was fine.........