I use SyncBack SE, which I am afraid is shareware rather than free, but can synchronise for network or local or ftp folders, or just compare with lots of customisation options, it can even be scheduled. It's for windows, and can be found at
http://www.2brightsparks.com/syncback/sbse.html
I have a lot of sites using DokuWiki and other text file based CMS's and it's ideal for backing them up as only the changed files a done and it can be used from PC to FTP to update files which have been edited on the PC.