There's an interesting article by Larry Garfield (Drupal's crell) about the planning process that Palantir uses before building a Drupal site. A big part of that process is a build spec in a spreadsheet:
The Build Spec is a Drupal-specific birds-eye-view of how the site will be built. It contains every content type that will be created, all fields, and all field, formatter, and widget settings (that is, the data model). It contains all Views that are going to be needed, and all of their displays. It contains every image style, every flag or nodequeue that is expected, every taxonomy vocabulary ... anything that you'd get from just pushing buttons.
I've done much of this myself when building sites (often when estimating sites), but in a much less structured way. I think I'm going to try using something like their spreadsheet with the next site I build.