Fribble - 12:40 am on Mar 28, 2010 (gmt 0)
Good stuff Mack,
I'd like to add that mapping or flowcharting software like MindManager or OmniGraffle can be great for brainstorming and writing down your file/site structure.
For the designing, my best friend is a huge whiteboard on my wall next to my desk. Lets me keep everything in view and easily modifiable.
And one of the most important things in my process, is determining what things the site absolutely has to have right away, and what can wait. If you try and put it all together at once it will be much more expensive, time-consuming, and complicated. Start with only the absolute must-haves and get it up and running, then build a timeline for the rest to be gradually added. Chances are you're going to modify that list of extras before you get them all done anyway.