WordPress should have a built-in mechanism for managing who can access what.
There's already plugins for it, like Tadlock's Members plugin, and I can't remember if it supported custom administration pages or not, but this should be in WP core, because we need a consistent and reliable API.
A plugin can 'register' a set of options (or it's administration menu[http://codex.wordpress.org/Administration_Menus]). WP picks it up and in it's access manager provides the options for the admin to choose who can access those options. The plugin can check weather current user have access to those options and do it's thing.
This whole API could be integrated with WP's Settings API, so if you're using Settings API you get the benefit of automatic access management for the plugin or whatever.