if its audio files you want to organize, i suggest you look no farther than Media Monkey (wow i sound like a salesman). But seriously, it is the best program to organize and retag music.
And, its FREE.
if you happen to have a mac around, you can use list view to manage files within a single directory tree. i do this frequently, mounting the volume as an SMB share remotely and managing the files that way.
tip: navigate one directory higher than you want to manage; option + turn down the folder arrow. this will expand all nested directories in one window. then, command-click the files you want to move en-masse. for example, if you want to manage files at c:\music\my cds, navigate to c:\music\ (on the mac remember) and opt-click the arrow next to the my 'cds directory'. this will expand every directory in my cds, in one window.
if this is a one-time thing, it might be worth investigating. if you regularly need to manage the files then maybe a windows solution may be worth waiting for.