My folder structure is a little byzantine but usually gets no deeper than three levels.
One thing that happens far more likely than I would like it is that sometimes I can inadvertently move a folder and drop it under another folder without noticing it. This leads to much fear and loathing until I find the missing folder in its new location.
Might it be possible to add a simple "Do you want to move xxx to yyy? Y/N" dialog to prevent this from happening?