Recent versions of iPhoto and Aperture have ditched the open folder system for a more secure "Library" format and, in Lion, Photo Booth takes the plunge as well.
The main reason for the switch from an open folder system to a closed, self-contained library is to keep more inexperienced users from breaking iPhoto by trying to "clean up" their computers.
The old iPhoto library was a mass of confusing folders, with dozens and dozens of folders. There were folders organized by date, with thumbnails, by master versions and more. Users who didn't know any better would frequently try to delete photos by going directly to the iPhoto Library folder and erasing files en masse. All they would do was break iPhoto.
Now all Apple's photo apps: iPhoto, Aperture, and Photo Booth have self-contained "libraries" to keep users out. The photos inside are only supposed to be opened by the applications that created them -- it's just like the file system on the iPad. Invisible, unalterable, and only to be opened by the application that created them.
Steve Jobs' quest to eliminate the file system continues.