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I also use an included page on every page of the site which, among other things, links to the homepage (with both text and logo graphic) In the alt tags of the graphic I add a keyword-rich statement that summarizes my site's intentions.
Additionally, at the bottom of each page, I have a link that looks like this:
Home l Top l Back
Therefore, I have a total of 4 links pointing to the home page on every page of my site. I estimate my site as having thousands of pages < 5,000. It is arranged in hierarchial, subject-specific structure as I described with a total of 4 links pointing to the home page (via different methods) on every page.
Interestingly, I layed out the linking structure of the site this way for usability, not for SEO.
Your thoughts?
Assuming that there are no dead ends on your site and there are no links to external domains, the total amount of PR (i.e. summing up the PR for each page on your domain) depends on the incoming PR and the number of pages. Therefore, if these things are unchanged your link structure will just decide how the PR distribute among your pages. Choosing a hierarchical structure as mentioned will lead to:
PR_Home >> PR_top level category >> PR_sub-category >> PR_content page,
i.e. the PR of your home page is relatively high, while it decreases rapidely.
The alternative would be a link structue where PR is distrubuted more equally over your pages.
I would not focus on PR distribution. As you said, you layed out the linking structure of the site for usability, not for SEO. I think that the best you can do.
To improve your ranking I would concentrate on the other factors as anchor text, title, ...
You seem to be emphasizing the fact that you have four links on each page pointing at your home page. There's nothing necessarily wrong with that, but of course it doesn't make your home page look any more important to Google, since any PR passed along is divided amongst the four links. The pages may look less cluttered with fewer "home" links, so you might consider cutting down to one or two.
You'll need, of course, to get other sites to link from you or the deeper pages may have such low PR that they won't get crawled. But that's just part of the job. I'd say stay with the layout you have rather than move to a flatter structure.