I would welcome any comments or alternatives approaches.

Internal Site Navigation -

Home Page: Html links to accessibility page + site map main page + all section pages + direct html links to a limited number of content pages such as popular, whats new, ... etc.
Javascript links to few items say a footer bar: feedback, about the site, ... etc.

Section Pages: Html links to home and accessibility pages + html links to all subsections pages or section content pages if there are no subsections.
Javascript links to other section pages in a header section + Javascript links to few items say a footer bar: feedback, about the site, ... etc.

Sub Section Pages: Html links to home, section and accessibility pages + html links to all subsections pages or section content pages if there are no subsections.
Javascript links to other section pages in a header section + Javascript links to few items say a footer bar: feedback, about the site, ... etc.

Content Pages: Html links to home, section, sub section (if used) and accessibility pages + direct html links to relevant links to other content pages (even cross section).
Javascript links to other section pages in a header section + Javascript links to few items say a footer bar: feedback, about the site, ... etc + Javascript links to next and last section/sub section pages and other content pages in the section/sub section - these are usually page numbers with a title on mouse over.

Site Map: Html links to all pages or to site map sub pages for larger sites.

Accessibility Page: Html links to home page + site map main page + all section pages + html links to any further accessibility information + html links to the footer bar items.

I know its not perfect but it

- gathers page rank (for whatever thats worth) up the heirarchy to the sub-section, section and home pages, okay the accessibility page gets it too.
- allows me to change header and footer text and links site wide by 3 changes - thats the home and accessibility pages + a javascript external script for the section pages and footer navigation.
- gives a breadcrumb trail visible to all.
- makes smaller content pages with the Javascript navigation ignored by most search engines leaving text and links high up the page for the search engines.

In case its not clear, I write the html and javascript by hand. For any of the majority of users reading this (I guess) can you control what your package generates - that is html or javascript links?