I’ve placed this book at the top of my list, as it has something for almost everybody. It starts by covering the fundamentals (and thus serves well as a desk reference), then moves on to tackle more advanced topics, such as testing and functional programming.
The second edition has been updated to cover ECMAScript 6 and does a great job of introducing you to its more common features. You also get to put your newly acquired knowledge into practice at the end of each chapter, as you build out a quiz app, adding features as you move through the book. I really like this project-based approach to learning and think it is one of the better ways to advance your programming skills.
A Beginner’s Guide to npm – the Node Package Manager
Node.js Web Development, Fourth Edition