Windows SharePoint Services (WSS) 3.0 provides branding through themes. A user can apply a WSS theme to a site to change its appearance.
In the July 2008 issue of MSDN Magazine, Ted Pattison walks you through a custom branding solution for SharePoint sites that leverages the capabilities of WSS to integrate custom Master Pages and custom CSS files at the level of the site collection.
You can browse the sample project that accompanies this column (or grab the download) and follow along.
Be sure to check out our MSDN Magazine archives for more articles about Office and SharePoint development.