If, as I do, you often need to use your image files with other applications or using scripts, you probably suffered from the so controversial file organization of iPhoto. This was a reason for not to use it. Using the script in this hint, you can export selected pictures from iPhoto, but they are linked rather than copied. There is no disk space waste, nor disparity between copies. Thus it is possible to organise photos in hierarchical folders, as you wish, while keeping the iPhoto library intact.
The script gives you a choice between aliases or symbolic links. If you don't know the point, use aliases. In some case however, neither aliases nor links are satisfying, because some applications are unable to manage and just ignore them. In those cases, you can use the third choice -- the script moves picture files to the chosen folder and replaces them with aliases. Use with caution, as side effects on iPhoto behavior are unknown. It is advisable to replace files in the iPhoto library before any modification on images. They can be moved again later.
Important: This operation is reversible. If run again, files are moved back in the iPhoto library and aliases are created in the chosen folder. More information in the script comments.
Download the script from macosxhints.com: export_links.zip
[robg adds: I tested the 'alias' option in the script, and it worked fine on my machine. I did not test the other two modes.]
Mac OS X Hints
http://hints.macworld.com/article.php?story=20040331181442748