An article I worked on has recently been published on MSDN. The article, Implementing a Brand in a SharePoint Server 2007 Publishing Site, discusses three options for deploying files used in branding a MOSS 2007 Publishing site including the advantages and disadvantages of each. Personally I strongly prefer the last approach, but it's good to see all your options. The paper does NOT talk about how to make your site not look like SharePoint.
Here's a summary on what the article is all about:
Microsoft Office SharePoint Server 2007 publishing sites are commonly used as the external face for companies and organizations. As the online presence, SharePoint publishing sites should employ a consistent appearance ("look and feel") to make navigation and discovery of information as easy as possible for users. Implementing a brand for a site, however, presents challenges. There are various implementation options, and each has advantages and disadvantages. However, it does not make sense for all projects to adopt the same process and technique.
Office SharePoint Server 2007 introduced the capability to host content-centric sites on the SharePoint platform. These sites, commonly referred to as publishing sites because of the SharePoint publishing features they employ, take advantage of a series of concepts and capabilities in Office SharePoint Server 2007 called Web content management (WCM). Publishing sites are frequently used in an Internet-facing scenario as the public face for a company or organization. Therefore, it is very important for these sites to have a consistent look and feel-also known as branding. However, the various options available for how to implement and deploy the site's brand can quickly confuse developers and designers.
This article explores what a publishing site project team should consider when planning how to implement a brand within Office SharePoint Server 2007. While many of this article's concepts and issues address Windows SharePoint Services 3.0 sites, this article focuses exclusively on Office SharePoint Server 2007 publishing sites.