I have created a base master page file that can be used for creation of new custom master pages. Microsoft provides this, but I ran into issues with this code and instead created a base file using components of default.master (that ships with SharePoint).
This code contains all the necessary content placeholders in order for the page to run. You can wrap your custom code around the placeholders and add your custom CSS file(s) in order to brand the master page.
The majority of the placeholders are labeled by area of the page or functionality. The rest are listed in the SDK, and are mainly superfluous placeholders that hold spacing images to create borders and margins. You will more than likely not be utilizing these, and you can move them to the hidden ASP panel located at the bottom of the file. Do not delete the ones you don't want to use, just move everything to the hidden panel. Without them all, pages in the SharePoint site will not render.
Click the link below to download a zip file containing the base master page file.
» Heather's Base Master Page
For more information about master pages and SharePoint, refer to:
» MOSS 2007 Design Component Relationships and Diagrams
» CSS Options with Master Pages
» Create a Feature: Master Pages for Site Collections