You're missing the whole point of iTunes, iPhoto, etc. The app ORGANIZES your files, but they're organized in the actual app, why would you care about how they are organized in the Finder?
For example, you open iPhoto and all your pics are there, you can sort them anyway you want... date, title, rating, etc. In the finder they're just in one folder, and sub-organized by year, month, day... but you're not suppose to be looking there, if you want to do something with a picture besides viewing it (like e-mailing it), then use iPhoto (not the finder), select it and click "Mail" at the bottom toolbar.
If none of the buttons in the toolbar offer you the action that you want to do (let's say you want to send it to a friend using a messenger) just drag it to the desktop and easily use it there. Stop looking for the files in the iPhoto Library folder!, that folder is there just to place them in one place, not to browse them. If you want to browse them then use iPhoto.
Don't worry about the iPhoto Library folder, that's doing OK in the background, all your imported pics are automatically placed there by iPhoto.
The exact same thing goes with iTunes, stop looking for your files in the iTunes library folder, use the actual iTunes app, that's what it was made for.
My point is, the idea is to worry about only one way to organize you files, so either use iApps to organize your files and let the apps do their thing in the Finder, or forget about those apps and do all by yourself in the Finder.
