The simple answer is everything! The site organization and content of your each and every page within your domain play a vital role in how your website is spidered and ranked.
Top Level / Category Themes
A top level theme is typically your primary subject matter or the “Main Category” of the site. This top category then feeds your lower pages with related content. An example of a web theme would be Rank By Design very own pages. In this site many subcategories of different kinds of optimization tools and SEO optimization techniques can be found.
The Rank By Design optimization tool pages are broken down into smaller pages using a common web theme as well. These pages might discuss different kind of optimization tools but the web theme always point back to the Main SEO Tool theme and then to related pages above this and finally back to the home page itself.
In the same way the SEO optimization technique pages point to all the related pages and tips on different tips on optimization and so forth.
The importance of a web theme is the organization of the main theme itself and how these links point to the inner pages. Therefore the way pages link to other pages and how they are organized, directly affect the heath of the site and in the end determine which page are primary and which ones are secondary.
Page Rank and Links
Now Page Rank is the way Google places importance into all your sites pages from links pointing to and within your domain. Usually the most important page is your index or home page and from there gets diluted though each inner page. See more about google’s page rank tool at wikipedia.
Page Rank is also determined by what kind of sites link to you: and the overall health of your site.
A common mistake is to have too many unrelated links on one page pointing to another with even more unrelated topics. This can dilute your Page Rank and your sites importance as a whole.