I think the most important thing is to start with the purpose of the Website. What are the messages, who are the traget audiences and what actions do you want them to take as a result of their visit to the website?
These are the boring parts of design but ultimately I believe they are the most important.
Too often they are ill considered.
There is a great post on this here:
http://minttwist.wordpress.com/2008/11/16/...fect-website-2/