I found a while ago that GoodSync was the best solution, however it is not really free with a very low limit of 100 files. I do not believe that software is worth $30, so I used AlternativeTo, and I was proven right with the quality of the free options available.

My requirements were the following:

1. Free
2. Ability to do offline backup on an external drive.
3. Smart one way mirror with comparison of destination
4. Configurable filters to not copy .svn folders for example
5. Support of multiple sources and destinations

Seems like a pretty low bar, but I was surprised not to find a lot of genuine candidates. I am listing below only the ones worth talking about, most solutions were online only, and the ones I do not mention in general had terrible UI.

FileMenu Tools ended up being my pick. I had the software already installed, but never noticed that feature before. The interface is simple and functional, it provides an editable diff of the two folders before operating, and filtering was as easy as you would expect. You can save presets for different couples of folders. The only option it lacks is a saved list of folders for batches, but it was good enough for me.

PureSync emerged as one of the best at first, unfortunately it felt like written in VisualBasic with a terrible interface, poor stability, and ineffective auto-update.

WinDataReflector did not give enough insight into what was done in the backup and synchronization processes.

Toucan was also promising but lacked clarity about the basic options, and handling multiple folders as separate projects was cumbersome, and the filtering was again not well integrated in the workflow.

GFI Backup allows to backup and sync folder, however the backup would work for mirroring but it does not compare what was already done the previous time, and the sync option is not flexible enough to be configured one way.