I recently came across an extremely handy open source API for managing settings in iPhone apps. In a nutshell, InAppSettingsKit looks and works just like the normal settings/preferences mechanism (e.g., Settings.bundle), except that it allows you to easily display a settings view in your app in addition to the standard Settings.app (there are a few other perks, too).
In addition to their website, you can listen to a great interview with one of the creators from via the “mac developer network” website.