The Patterns&Patrices group is providing information on how to build SharePoint Intranet applications at http://www.codeplex.com/spg . The site provides regular alpha drops of a reference implementation (a training management application) that demonstrates how to correctly use SharePoint as development platform - take a look at SharePoint guidance Vision and Scope document for more information.
We plan to provide guidance to customers on how to build SharePoint Intranet Applications. This includes guidance on how to Architect, Design, and Develop applications as well as best practices.
This guidance is intended for software architects and software developers who are building applications on Microsoft Office SharePoint Server. Familiarity with Windows SharePoint Services, Microsoft Office SharePoint Server, and ASP.NET is useful for evaluating the guidance.
Take a look at the latest drop - SPG Drop 9-9-2008