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For example, do we go with the 'tree' where your index page is at the top then followed by the subdirectories, then product pages etc...or is there any other linking systems that can be followed when designing a site that are known to work? ie. perhaps a design specifcally for 'funneling' PR?
I'd like to quote a post that Robert_Charlton just made in another thread:
Study the home page nav structure of dmoz. It links to main areas, plus roughly 3 of the most popular major subcategories of each area.
So, both users and bots are directed efficiently to sections that would get the most searches. Each of these sections then has its own menuing system, directing users and bots to the next levels. It's a great example of how to make what works best for users work best for SEO, and vice versa.
Assuming that structure:
Linking the sub pages and category pages to one another dilutes the page rank given to the home page. Most sites do this and can be optimized to increase home page rank, however usability concerns usually are an obstacle.
To maximize PR home page, the home page should navigate out to every page via a site map and then everything should link back to the home page and only the home page, but in practice that is not a usable structure.
I've considered using a site map and sub pages and rel=nofollow to kill the unhelpful links but yet to find a client or appropriate site for such an approach.