I don't know of any. What problem is iTunes causing for you?
I find that I can use iTunes interface to do anything I want with my music collection. I have never found the need to muck around in the iTunes folder to change anything, and I don't care how it's organized.
But, if you have a specific problem, maybe someone can help you with it, if we know what it is.
iTunes works fine for me since Apple bought SoundJam.
There was onetime at iT v5 that I have a problem - out came v6 and I have been void of problems since.
Now - what is that iTunes is doing that is causing problems for you?
If you have the options in iTunes prefs>Advanced - keep and copy - selected then iTunes will do the work for you. Remember that iTunes is a data base manager - any moves made of files in the Finder are moves that iTunes can follow. I suspect that if you are moving things outside the iTunes interface then you a creating your own problems.
Long story on how I got to this point. But I actually I just made a little headway.I just opened itunes and it said it couldnt find the library so I went and located it.Now I have all of my music listed but when I go and try to listen to a song it says this song can not be located so I locate it and that song will now play.I now need to know how to locate all the songs at once I do know where they are.
Tried Songbird? It's not perfect but might be an alternative.
Personally I don't like iTunes because some small details...
No possibility to create smart playlists based on path.
Not able to use Album Artist in Column Browser.
The non standard list-selection (shift+up/down arrow does not follow standard behavior).