Great example of using WordPress as a Web Application Framework: The Lift team re-worked the WordPress admin into a project management application for Frito Lay: Frito-Lay Creative Project Management App – Lift

One of the biggest tasks was re-skinning the admin. We removed all WordPress branding and converted it into a white-label, custom CMS. The front-end is redirected to the admin and requires user authentication to sign in and use the app. Once logged in, a custom logo and admin bar greet the user with a soft color palette and refreshing design. The traditional Publish metabox has been completely replaced with a custom one which factors in the custom workflow mentioned above.
~ Frito-Lay Creative Project Management App – Lift