as berli said, you can already make multiple save directories, but limewire wont automatically send video files to one folder, audio to another, etc. That you have to do manually. i dont think that it would be very hard to program limewire to move video files and audio files into seperate folders, but there are so many different types of files that it might not recognize something as a video file (such as a .zip ifle) and would get placed incorrectly. The best way to do it right now is as berli said:
I. My shared folder
a. audio (subfolder)
1. Jazz (subfolder)
2. Alternative (subfolder)
b. video (subfolder)
c. images (subfolder)

Thats the easiest way, although i do agree with you on needing a organizing system (like in kazaa).