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Method 1:
Index page with one outbound link to a (map) page. The map page has 48 outbound links to (content) pages. The content pages have one outbound link to the index page.
I ran this through a PR calculator and the index page gets most of the PR but the map page also gets allot.
Method 2:
Index page with 49 outbound links to (content) pages. The content pages have one outbound link to the index page. I ran this through a PR calculator and the index page gets more PR than in method one. I don't trust the PR calculator I used and would appreciate some human feedback on this. So which method would be better or is there a better way than what I have mentioned to get the bulk of the PR focused to the index page. Thanks
I wouldn't trust any PR calculator nowadays. PageRank is most likely being calculated differently now than any of those PR calculators. The PR calculators use the old PR calculation, as originally published. Google doesn't own the PR calculation, they only own the trademark for the word PageRank. Some big California university owns the patent on Pagerank. Since Google, Inc. doesn't want to pay that big university huge royalty fees, it's most likely that they came up with their own PR calculation recently.
Basically you are asking, if only one link was in question, which is better for page1:
page1 links to page2 links to page3 links to page1
or
page1 links to page2 links to page1
It's better for page1 to not to go through an extra step.
You really have two basic options although there are lots of variants to play around with.
(1) Link all your 50 pages from the index page in which case you don't need a site map. This spreads the PR evenly between the pages and if they link back to the index page maximises the index page PR. You also don't waste PR on a site map.
The index page doesn't need to be a list of links. You could have the most useful placed prominently for easy navigation and the remainder as less prominent. But probably 50 pages is about the limit for this sort of layout.
A disadvantage is users will have to go back to the index page to get to another page, unless you interlink all your pages.
(2) Divide your pages into themes, link to one "head" page in each theme from the index page, interlink all the pages in each theme, and link back to the index page from each page. This layout benefits from a site map. For easy navigation you could interlink the themes at the head page.
This layout gives you (approximately) a PRx, PR(x-1), PR(x-2) scenario. But if you get deep links it tends to boost the PR of the theme linked to.
I agree with bhartzer that linkig from your home page to your most important pages is sensible, but the trademark issue is a red herring IMO.