I have seen lot of articles about customizing master pages of MOSS 2007. But all were talking about basic customization. What happen when you want to totally brand the pages. The best way to do so is to develop a theme for MOSS & write a brand new masterfile without copying the default master file. This is a nightmare with Sharepoint designer, because you cant easily identify the css elements and html elements.
The solution I found was using the IE developer toolbar. It was the savior for me.
You can download the toolbar from here.