I recently read WordPress Web Application Development by Rakhitha Nimesh Ratnayake.  You can get your copy here:

http://bit.ly/1e3ioxG

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.