First of all, define a back-up strategy, defining:
- Back-up data (What to copy)
- Back-up frequency (Schedule)
- Back-up automation (yes/No)
- Back-up type (Complete, incremental or differential) 
- Back-up back-ups (Number of copies and location)

You can use tools like:

Disks:
Make backups as HD image in img format.

rsbackup:
Backups are stored as complete filesystem trees on a (perhaps external) hard disk.  Multiple backups use hard links between identical files to save space.
Backups may be taken from multiple machines (over SSH) and stored to multiple disks.
Backups may be made automatically, i.e. without relying on the operator to remember to make a backup.

Clonezilla:
Make a backup from this live DVD backup tool.

Partimage:
Make local and over the network partition backups and restoration.

Rudiments backup:
Backup using shell scripts.

Manual backups:
There are more solutions, but in my case for system maintenance and especially for backups, my manual procedure is all right.


My Debian Workstation back-up procedure is very simple. 
Remember to keep the directory/file permissions and symlinks using the command 'cp -dpR':

/etc
Reasons:
sudoers
fluxbox/
apt/
hosts
resolve.conf
network/interfaces
kvm/
firewall script
more...

/home/esteban/Documents
Reasons:
All my docs are here

/var/cache/apt/archives:
Reason:
Contains all the DEB packages, except for after a new system have been installed from netinstall Disc (at leat)

/home/Esteban/Downloads/to Debian 8 Jessie repo
Reason: The directory is the new mini-repo of packages downloaded to put into 2 remote/external HDs/SSDs repository directory called: Debian 8 Jessie repo


Notes:
I don't backup these directories:

/usr
Reason:
I don't back up this directory but contains more software installations and configurations

/opt
Reason:
I don't back up this directory but contains more software installations and configurations

/home/esteban/Downloads
Reason: I don't keep files in this directory. I put away the files in remote/external HDs/SSDs the weekends to free system space.

/home/esteban/
Reason:
To much files to backup. I restore virtual machines templates from a Virtual Applicance directory in a remote or external HD/SSD. In this case I can backup just the virtual machines to my VM backups or create/merge a templete.
Hidden files
Hidden config files
VirtualBox VMs/
Documents/
Downloads/

/var/lib/libvirt
Reasons:
KVM virtual machines, qcow2 containers and ISO can be restored from here, but there are to much files to backup, and I restore virtual machines templates from a Virtual Applicance directory in a remote or external HD/SSD. In this case I can backup just the virtual machines to my VM backups or create/merge a templete.

/boot
Reason:
grub/
I can restore Grub manually, from the installation CD/DVD or using tools like Knoppix live DVD or another rescue CD/DVD.