I found Konqueror very good if you want to organize a lot in your own data (copy, move, map, etc.). In Nautilus you can not see the full directory structure (actually only one, the current one). So in Nautilus you need two or even more windows to keep track.
I completely rearrange my files in a new directory tree based on the 5-folder principle (eg, 2.3.1 to 2.3.5), so I have to rearrange old files in this new structure. I need to know if a file should be copied where it needs to be stored. In Konqueror I see the directory tree and can choose between several candidates.
Who knows a practical solution?