I have a website that shows galleries. Users can upload their own content from the web (by entering a URL) or by uploading a picture from their computer.
You can save your trusted data just in parallel of htdocs/www folder so that any user can not access that folder. Also you can add .htaccess authentication on your trusted data (for .htaccess you should kept your .htpasswd file in parallel of htdocs/www folder) if you are using apache.