I spent a good part of 2004 branding a SharePoint Portal site for a client. Much of the work involved in branding Portal is undocumented, so I spent a lot of time using the old trial and error method.
Now, Daniel McPherson has created some documents on Branding Portal. Check them out:
Office Developer Center: Branding a SharePoint Portal Server 2003 Site: Part 1, Understanding the Use of a Corporate Brand
Office Developer Center: Branding a SharePoint Portal Server 2003 Site: Part 2, How to Apply Your Own Corporate Brand
Very good information. I just wish I had these articles in hand 9 months ago! :-)