In the current version of SharePoint, advanced customisation of the look and feel can easily be a very complicated task. With smaller deployments you can often get away with using the power of FrontPage 2003. However, when it comes to larger deployments with hundreds of team sites and/or portal areas, you face some real challenges. There are basically two different ways of approaching this. Either you go down the track of custom templates or the track of site definitions.
The custom templates are the ones you create by customising a site through the UI and then saving it as a template. This is straight forward to do, but the biggest drawback is that sites created from custom templates have no link to the template once they have been created. As a consequence, you cannot modify existing sites by making changes to the template.
Site defitions, which are sitting on the file system of the front-end web servers, solves the problem of being able to make changes that affect all existing sites. The trade off with site definitions though is that they are complex and time consuming to build. It requires lots of CAML editing and even simple layout changes have to be carried out in potentially hundreds of different HTML files. The site definition for the default team site contains 97 HTML pages with lots of duplicated HTML across most of the files.
The next version of SharePoint, which is included in the 2007 Microsoft Office release towards the end of this year, will be build on ASP.NET 2.0 master pages. This fact alone will ease customisation substantially. The master page will typically contain the branding, header, footer and navigation for the site. You will be able to redesign an entire family of sites, by modifying the master page.
Apart from master pages, SharePoint 2007 will have other improvements that will ease customisation of the look and feel. These include new and improved web parts and web part zones as well as the page layouts adopted from MCMS 2002. The SharePoint Team Blog has a good post on how the new SharePoint pages will be composed. The upshot is that it will become more realistic to train up creative designers to build SharePoint layouts and I believe we will see some very sexy SharePoint implementations in the future.