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-long switch may help you.
#the best way
genisoimage -o /tmp/Backup-Myfiles2.iso -U -iso-level 4 -R /source/dir
This was the only way I could get unmodified long file names and VERY deep directories onto the iso image as original otherwise they get renamed and truncated which breaks a lot of things and makes it confusing. But be warned this breaks the iso9660 standard so many OS's especially Windows may not be able to read it.
#this fixes it
-R is for Rock Ridge and allows for more than 8 deep folders
-U allows for untranslated filenames
genisoimage -o /tmp/Backup-Myfiles.iso -R -U .
#with an exclude
genisoimage -o /tmp/Backup-Myfiles.iso -R -U -m WebSites/blabla .
Warning: creating filesystem that does not conform to ISO-9660.
I: -input-charset not specified, using utf-8 (detected in locale settings)
#the -m causes a shrink error unless you put it earlier
genisoimage: File 'blank.html' did shrink.
Files must not be changed while genisoimage runs!
-m WebSites/blabla -o /tmp/Backup-Myfiles.iso -R -U .