After speaking with several developers and partners around the world, I decided to blog this instead of sending emails to all of them every time. Please let me know if I am missing a critical resource.
Since Office has adopted the new HTML + JS model for developing Office Apps, there has been a lot of demand in learning this model and understanding how it fits in the traditional model. The Office Store App model is designed for portability of your apps across multiple kinds of OS. The same app will run wherever Office runs. My personal favorite is the Outlook Contextual App because it enables new scenarios and ways of reaching to your end-user.
When it comes to Windows, HTML + JS is a boon. I have seen a D3.js visualization working in a native Windows Store App like a charm in no time.
Microsoft Virtual Academy
Windows 8.1 UX Design Jump Start
Windows Store Apps with HTML5 Refresh Jump Start
Advanced Windows Store App Development with HTML5 Jump Start
Cross-Platform Development with Visual Studio
Free Book (a little dated but the concepts are still valuable)
Office 365 Apps
Deep Dive: Integrate Office 365 APIs in Your Mobile Device Apps
Introduction to Office 365 Development
Finally, there are two sites that cover these topics in detail including design and development guidance.
Have fun developing!