[eluser]JoostV[/eluser]
I'm with Bramme on this one. I like front end and back end to share models and libraries. Some methods you will only use in back end, such as delete(). But many methods will be shared. Sharing models and libraries helps you to write less redundant or repetitive code.
Of course, it is still possible to create a backend_config.php and a frontend_config.php, and even seprate helper files if you need to.
Furthermore I would remove /system and /applications from you webroot, for security. This would leave you with:
-applications [folder]
-system [folder]
-webroot [folder]
-index.php
-.htaccess
-robots.txt
-skins [folder]
