I have pulled together a list of items in SharePoint 2007 that may haunt your custom branding if you don't take special note to address it in the interface. Often while branding SharePoint you can get wrapped up with just working with a single web page while changing your design. There is a large application to worry about and this list will hopefully help you avoid bits and pieces of the old SharePoint look popping up on you after you are done branding SharePoint.
If there are other elements in this list that have caused you grief, feel free to share.
Page elements to double check while rebranding SharePoint