Add a system-wide preference for page ids you don't want displayed by wp_list_pages() and check for this preference value in the core wp_list_pages() function call.
I typically add this to the theme I'm using (by adding the exclude parameter to the wp_list_pages() call in the theme's header. I do this because I've got a few pages I want accessible via a link I'll give out privately, while not burying them as a child page.
