I recently read WordPress Web Application Development by Rakhitha Nimesh Ratnayake. You can get your copy here:
As the title implies it covers using WordPress as your application framework. I highly recommend this book even if you are not building a web app. The author does a great job of breaking down complex development techniques that are useful regardless of how you plan to use WordPress. I found learning about how to use built in functions the most helpful. Did not realize how much WordPress provides for you as far as development goes.