The folks at Voltronik have put together a pretty interesting case study going over their processes and considerations for building a project management system for a client, managed on the front end, all with WordPress.
The result is a Bootstrap based UI, but it appears to have included some pretty advanced backend code to properly allow the client to view, edit, and manage various aspects of the project management application.
I love seeing case studies like this. Now, I only wish some of the code were publicly available. One part is though; their Better notifications for WordPress plugin, which they built for this project, looks pretty interesting, and I look forward to giving it a test run.