This pages links to recommendations and notes about how you should set up your application:
SitePage -- How to create a master template for your site.
Directory Structure -- Notes on how to create a robust directory structure for your site.
ModelViewController -- A paradigm for keeping content, design, and code separate.
Web Style Guidelines -- Links and notes related to good hypertext style.
Managing The URI Space -- Creating persitent, meaningful resource names.
Model Two plus One -- An example of using the Logic / View + Actions design
See also: Webware Recipes