don't know why you'd want to tbh, esp if the backup partition is to be on the same hard drive as your system.
I tend to set up machines with a seperate /home partition, that way I can safely hose the system or install a fresh system, even install a completely different distro and the stuff in /home won't be touched
Although to answer you're original question, probably the best way to do it is to set up a cron job to dd or copy the directories/partitions you're wanting to backup, preferably to a separate hard disk or even to a separate machine using scp/rcp.