I wrote an article for dev.opera.com titled intelligent site structure for better SEO. Go check it out!
Intelligent site structure for better SEO
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By using a correct en logic navigation structure …
Use also sub navigation with link to mainpages, etc. Recommend to use a sitemap (e.g. Google Sitemap).
Henri: a google sitemap is not always a solution and has NOTHING to do with your site structure, and there’s a lot more to it than you just pointed out :)
I’d say, read the article ;)