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I for one am to the point of placing all pages within the main directory structure, even though this is not such
a stellar way in which to design a website.
There is a well known Google employee with a blog that is a great example. Look at the PR on Matt’s, I mean his, website. The .com is at PR 5 while the .com/blog/ is a PR 7.
However, the length of the shortest click-path to get to a url from an external link is important, because it helps to determine Page Rank. As BillyS said, on many sites the number of clicks can be closely correlated with the directory structure. But it is the links that matter, not the forward slashes.
If you "always" ask for a link to the main root, then naturally this is getting the most PR.
However if you have a great sub directory, try building incoming links to it.
I have had pages in subdirectories actually "out PR" the homepage before, it's all in how people link to you.