In iTunes 9, there's a new feature that remedies this organization problem, appropriately named iTunes Media organization. It moves your folders around into a much more logical structure, with separate folders for audiobooks, iPhone apps, movies, music, podcasts, ringtones, TV shows, and voice memos.
Another extremely useful organizational feature that's come out in iTunes 9 is a new folder named "Automatically add to iTunes." This folder does exactly what it says; drag a file into it, and not only will it be added to iTunes immediately, it will also automatically move to the appropriate folder. So, for example, if you drag a movie file into the "Automatically add to iTunes" folder, it'll show up your iTunes library immediately, and it'll also automatically move to the iTunes Music > Movies folder. This makes it easier than ever to keep things organized.
Sweet, sweet organization, how I love thee
The "Automatically add to iTunes" folder is enabled automatically when you install iTunes 9, and is located in the /Music/iTunes/iTunes Music/ folder for each user on the Mac. This happens whether you enable iTunes Media organization or not, so all you'll be losing by not upgrading to the new organization scheme is the peace of mind of having a far less cluttered library in the Finder. Unless you're a fiend for organization, it might not be worth the hassle of backing up your entire iTunes library again.
Note to readers: the last paragraph was rewritten to clarify how the Automatically Add to iTunes folder works, how it is enabled, and where to find it.