There are a number of different ways to create customized MOSS publishing sites - through the web UI, SharePoint designer, Visual Studio Extensions for SharePoint, and so on. But sometimes these aren't enough - you just have to build it from scratch yourself. This means diving into the world of custom site definitions, features, xml configuration files, master pages, and the myriad of bits and pieces that SharePoint brings together to work its magic.
In WSS, this process is fairly straightforward (with the exception of deployent via features which can be a bit more challenging) but MOSS is a different animal. The Publishing architecture adds a layer of complexity that can be daunting for new designers and developers. Once you understand how all the moving parts work together it's not so hard to grasp but it never hurts to have a handy step-by-step guide to help you alaong te wa.
So here it is - Basic MOSS Publishing Site Definitions 101. This guide is designed to help you construct a simple site definition, deploy it as a feature, and get up and running in as short a time as possible. It doesn't cover every situation and you may well have more complicated requirements but the basic principles are valid for even the most complex sites.