If I say backup I usualy mean dumping a whole filesystem, a content of a partition.
If other filesystems are already mounted to this filesystem, the "tar" will pack them as well. There are some magic switches for tar to stay on one filesystem, but then folders hidden by the mount will skipped.
My solution follows.
Mount the filesystem with option "bind", and dump the binded folder.
# mkdir /mnt/rootfs
# mount / /mnt/rootfs -o bind
# cd /mnt/rootfs
# tar cjf /mnt/backup/rootfs.tar.bz2 .
# umount /mnt/rootfs
Where /mnt/backup is an other partition.
It is also a good idea to duplicate your root partition to an other partition located on a secondary disk. In case an emergecy you can boot your system from that disk. Note that you should make that secondary disk bootable with a proper boot option. "/etc/fstab" should also be modified.