This blog posting applies to Microsoft Office SharePoint Server 2007.
This is a topic near and dear to my heart. I've spent many hours helping customers plan and execute a wide range of customizations for MOSS 2007.
Now, the ECM Team (Enterprise Content Management) has published an exhaustive paper on these topics. At least, I was exhausted reading it! No, really, it's a great guide and covers so many areas that normally don't even get touched on.
Announcement and request for feedback: http://blogs.msdn.com/ecm/archive/2008/03/11/announcing-design-and-build-sites-for-office-sharepoint-server-2007.aspx.
This is a tremendously valuable resource, go get it!