I'd take a look at this:
http://www.aboutmyip.com/AboutMyXApp/DeltaCopy.jsp
It uses
rsync, which has become the standard command-line backup utility in the *nix world. It's very cleverly designed to minimize the amount of copying involved. The author is a very smart Australian fellow named Andrew Tridgell who was also responsible for creating "Samba" which emulates a Windows file server on Unix platforms.
I have rsync scripts that run nightly to make backups over the Internet. I back up my public servers to a machine in my house along with my local file server where I keep all my work and email.