For the majority of organisations and businesses, branding of SharePoint sites will be essential. There are a few strategies to implementing branding on SharePoint sites, including but not limited to, master pages, page layouts and CSS. Master pages define the shared elements to the site, such as logo, navigation and footers, while page layouts offer a powerful and flexible way to mange the overall look to the sites pages. CSS is used to control the overall display of page elements, including images, fonts, layouts and page structure.

This¬†article goes into detail about SharePoint customisation. It’s split into three articles.
Part 1: http://www.sharepointpromag.com/article/sharepoint/sharepoint-branding-101-how-to-implement-a-custom-branded-site-129843
Part 2: http://www.sharepointpromag.com/article/sharepoint/sharepoint-branding-master-pages-136262
Part 3: Coming Soon.

Another useful article I read about SharePoint Branding can be found at: http://www.heathersolomon.com/blog/articles/brandsppart2.aspx