Windows only: Free, open source application FlickrSync monitors any image folders of your choosing and syncs their contents to your Flickr account. We showed you a simple command line method for automatic Flickr uploads, but FlickrSync brings an entirely new level of functionality to keeping desktop folders in sync with your Flickr account—allowing you to do things like match folders to Flickr sets and create new sets for new folders.
It takes a little getting used to, but with FlickrSync you can basically manage your photos locally and ensure the results are replicated perfectly on Flickr (which makes it an exceptionally good photo backup tool). FlickrSync is a free, Windows-only download requiring .NET 3.0. If you need to recover photos in the other direction (i.e., from Flickr), try previously mentioned Migratr.