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If you want to follow the Linux Filesystem Hierarchy standard then somewhere under /mnt is appropriate for temporary mounts and somewhere under /media is appropriate for removable media (a USB HDD might count as removable media; an internal HDD would not).
A separate HDD would guard against primary HDD failure alone; it would not guard against events damaging the entire computer (such as fire); for this reason external media is a more robust choice and off-site storage even better.
EDIT: the directory hierarchy under each /home/* directory is for files specific to the associated user.
Last edited by catkin; 05-21-2011 at 09:01 AM.
Reason: missing space
If your intention is to have the backup filesystem permanently mounted, then I'd be inclined to avoid both /media and /mnt.
/mnt is intended to be used for temporary mounts done by the system administrator, so for example
mount /dev/backupdrive /mnt/backup
would be an appropriate use of /mnt
/media is where the desktop environments will automatically mount removable media via udev + udsks/hal. Label a disk as "backup" and it will be mounted on /media/backup
For this reason I prefer to aviod using /media directly and leave it for udev/hal.
For permanent mounts, what I do is I have all my local filesystems mounted on subdirectories under /local.
... and so on, but it's really up to you to decide how you like to organise it. It doesn't really matter what scheme you come up with, but if you do think out a scheme and stick to it, it'll make your system much tidier and easier to manage in the long run.
Just be aware of, and respect the intended use of /mnt and /media and you should be fine.