But remember to maximize PR, do not cross link between subdirectories. Only link back to the home page. Use a <BASE href="http://www.example.com"> on all pages and only use the <a href="/">home page</a> as the internal link back.
It is something you don't need to worry normally - just make sure you structure your website logically and in a manner that is useful for a human user. That includes that you link into your root directory (where the index.htm/.html/.php lives) from every page.
All advice beyond that is SEO alchemy in my opinion. I do link among subdirectories where it makes sense, don't use a base href and I don't think it does me any harm.