I've optimized my storing procedure. I've adapted it from the hierarchy of building websites and how the files are stored.
Top level folder: Music
Inside Music: beatport, traxsource, stompy, masterbeat, etc.
Inside beatport, labeled by date of purchase: 12.21.09, 01.05.11, 01.25.11, etc...
***Then I upload the folders to a server for storage.
I've found that storing it this way help when transferring music to an external hard drive or replacing music on another computer. Also, with the music being on a server I can download the most recent dated folders and play a set anywhere, without having to have my computer or external hard drive with me.