Did you know that Microsoft's patterns & practices group is working on SharePoint guidance? You can view their work as it is developed on the CodePlex site: http://www.codeplex.com/spg. In addition to a reference implementation, they are working on documentation that discusses the trade-offs and decisions that go into a SharePoint-based development project. There are many decision points, so they cannot obviously cover everything. So be sure to post your questions and comments so the team knows where to go next! I had the privilege of meeting with them this week along with a few MVPs and together we brainstormed some areas to pursue. But your feedback is just as important -- please speak up.