From Digital Web Magazine (a reliable regular read), this article discusses the thought process behind designing a website. Written from the perspective of the web developer, it's also a good introduction for clients.
This is a good article for nonprofit-type folks who are thinking about getting a website.
Here's a bit:
"Interestingly enough, most of the sites I work on don't have the goal of making lots of money. Most of my sites are communication sites, so the goals become a little more complicated. I try to take what the client wants to do and put it in a few sentences of goals, like "cut down on phone calls about the posted schedules, let users know how to get a personal trainer, and present a sophisticated portfolio."
Read the article: Digital Web Magazine - Creating a Site Design Plan