In general - SpiderOak will synchronize any folders that it can backup (including network drives, external drives, USB Keys, and so on).
However, some folders might not be a good idea to synchronize -- such as application data folders. The reason for this is because many applications cannot handle having another process change their data files. These include programs like iTunes and iCal. To provide an example, you can synchronize your music folders without problem but you may have trouble synchronizing the iTunes database of songs.