The way I do it is starting with the logo.

I have a graphic designer work with me on the logo. With the finished logo you get style guidelines and an entire kit of all logo formats and resolutions.

You also get:

1) Color scheme - primary and secondary colors (this article reinforces this as well)

2) Typography - primary and secondary fonts. Now your use of any fonts especially custom fonts is no longer arbitrary, and congruent to a theme

3) Evocative messaging. The logo already evokes something in the viewer, the site is now congruent to that

This gives you a great launchpad and highly combustible accelerant to propel everything forward.