[Skunkworks] How do you organize data in your computer?

Hi guys, I am increasingly finding it more and more difficult to avoid duplicates, especially images, audio and downloads. My downloads folder generally is full of pdf's, torrent files and images, just wondering, is there a time tested way of ensuring valuable disk space is not wasted in duplicated? On other news, who knows of a good app that would run in the background and organize my machine? :-) sent from my disorganized laptop.