Do you want to focus more of your weight on your home page, or on your sub-pages? Is there a certain page you want to emphasize? How do you want people to find your site in the search engines? The answers to these questions should shape how you lay out your site's linking structure.
I feel that this topic is best explained via examples and so I will now present a series of examples of different site structures and what they mean for you.
The first example is a pyramid or hierarchical linking structure. The index page links to sub-sections, which then link to their own sub-sections, and so on down the line. Each individual page on the site links to its parent page, and it's children pages, in addition to the index page. You'll find this linking structure on directory sites like DMOZ.org.
Since every page of the site in this example links to the index page most of the PR is focused on the index page and the deeper you go into the linking structure the less PR there is. This type of structure is appropriate for sites that are optimizing their home page for some keywords, or larger sites that are unable to pull off other linking schemes. This same linking scheme can be applied to sections of a larger site if you want to concentrate PR on a specific page. If you use this linking scheme and put keywords in the text linking back to your homepage, or the top of your pyramid if you're applying this scheme to only a section of your site, the benefit is enormous.