The Patterns & Practices group at Microsoft has just released SharePoint Guidance documents. This is Microsoft's recommendations for how to design, develop, deploy and operate architecturally sound applications on the Microsoft platform.
This guidance documentation set is targeted at helping you build intranet applications with SharePoint. It's not just a whitepaper. It includes a reference implementation of a training management application built on SharePoint. Meaning you get a better understand of not only the technical details of how to implement the solution, but also the architectural decisions about patterns, factoring, and packaging. You'll also see the design tradeoffs that you will likely encounter when creating intranet applications with MOSS.