I'm using Beyond Compare to back up at the moment to my NAS. It's directory sync mode works much like you describe except it works out what is out of date when you are ready to back up rather than tracking this in the background. Once it has finished comparing the two copies (I set it to compare size / modified date time) you can then mark folders you don't want to sync. Beyond Compare isn't free though ($30 for the standard version), but perhaps a similar folder comparison tool is out there for free.