I wouldn't say I go as far in depth as you guys are talking about, but I do follow several rules for improving UX.
- Everything important should be within three clicks of the main page.
- Really important things should be as close to the top as possible.
- Secondary items should be off to the right edge of the page because they don't get in the way.
- If some guy I pulled off the street can't find what he's looking for within 30 seconds of landing on the main page, and it's not arcane, I'm doing it wrong.
- The difference between navigation, content, and advertising should be obvious.