Craig,
I love your topic.... and you have addressed so many points that made me smile.
Before you begin to design your web site, you should have a vision a theme of what you want. If you are a web developer/ Designer.. you have to have the ability to interpret your clients dream and put it on code. Whether you are creating the whole web site in Fireworks or Photoshop, your theme should be established from the begining.
The functionality of your web site should be addressed from the begining. As far as navigation buttons, DHMTL pop up screens (better than Javascripts)... Forms, what type of information are you going to collect from your customers? if you`re going to collect important information, what are you going to do to protect your customers valuable information (SSL Cert?)
BUT.... for most of the part, what you need to worry about is the content. What are your topics, your keywords, What are your products, what is your GOAL....
Although the layout of your web site is very important make sure you have the content to go along with it. It would make your web site stand out more and people would feel confortable doing business with you.
here is what you need:
1. A good Designer/ Developer
2. Good Content
3. SSL Cert if needed
4. Domain should be easy to remember.

A web designer told me to do many things, like shop for a shopping cart. I really thought the cart was part of the pages and then was amazed at the variety available.
I was also amazed at how much can be done by a novice--registration etc.
Yes, you really do need to thing before coding. Would you build a store, or a conference center (if you are not doing the store) without a plan?
Craig L,
Just like with your business plan, you have to plan your web site. Especially if we go into the area of Functionality and collections.
Collections:
I hope this helps you some...