I do a http://clonezilla.org/
image of my system hard disk after each apt-get upgrade. I do this for two reasons:
1. Drive failure. I have an image that I can restore fully configured and ready to go
2. Update issues. If for any reason an apt-get upgrade does anything I don't want, I can restore the image.
For the media drive, I have a freenas box running in my workshop. I use rsync nightly to back up the media drive in the core. Since it is in a different building on the property, I have a (sort of) off-site backup of my media. I have thought about using RAID5, but RAID is still not enough and I can get a full backup with just 2 2TB drives.
I have tried the system backup and restore on to a VM test core, I was not able to get it working.