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Disagree all you like, but it is more than a theory. Most get practical results out of it.
>>I have certain directories within our site that are virutually identical to other directories.
Do you mean those directories have pages with virtually the same content?
If so, I urge you to read here [webmasterworld.com] for a little while. Duplicate content can harm a site.
Enjoy!
Us webmasters would be pounding their servers working out PR + links on our sites and all competitor sites! Then be working out all the on the page stuff and to fluff those SERPs up ;)
If you want to search for your site and its not returning any higher PR links with link:site.com then just type site.com and click on "pages that contain the term"...works for me.
Also, those older threads about working out the log....maybe if all links were shown that would leave the algo exposed a bit? I don't know....either way it seems <PR3 links don't have much sway.