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Now granted, most of them may very well have been problems with certain programs and linking to bad neighborhoods...but some PR0 toolbars may not be any penalty at all.
I've heard of the possiblity of www.examplewebsite.com/a/b/c/d/examplepage.html being a PR0 (all white toolbar)
This could be caused by the fact that if:
www.examplewebsite.com = PR5
/a=PR4
/a/b=PR3
/a/b/c=PR2
/a/b/c/d=PR1
/a/b/c/d/examplepage.html=PR0
The above example only assumes this: www.examplewebsite.com/index.htm links to www.examplewebsite.com/a (index>A)
Then A>B, Then B>C, Then C>D and of course D links to examplepage.html
Now for all practical purposes, this makes sense.
I am also intrigued by another possibility of a PR0:
www.PR9.com/index.html links to www.brandnewwebsite.com/index.html (where www.brandnewwebsite.com/index.html is not indexed yet.)
The fact that a high ranking page, which is spidered often, is linking to an unindexed site may be a reason for a PR0? it's almost like google is saying, "For a PR9 to link to this site...it must be important, but before we give it any PageRank...let's be sure"
Are there other examples of a NON-penalty PR0?
The toolbar resolution between 0.00 and 1.00 is unknown. There is such a thing as a high zero and a low zero, which cannot be seen on the toolbar, but can only be deduced from ranking comparisons over time. Assuming that your on-page characteristics are excellent (extremely specific keywords that hardly exist elsewhere on the web, and you have them in the title, in a headline, in dozens of anchor texts on your internal links, and in the filename -- everything is perfect!) -- assuming excellent on-page characteristics and extreme keyword specificity, then there is a massive difference in your ranking when you compare a low zero to a high zero. That's a fact, not speculation.
My educated belief is that there's a threshold within what we see as a PR0 on the toolbar that is quite significant. Below this threshold, your excellent on-page characteristics get clobbered. Above it and you are suddenly competitive.
Having said that, I believe that it's possible for pages that have not been deliberately penalized to fall below this threshold, simply because there isn't enough PR for them to inherit. When that happens, it might as well be a penalty. But if you can do something to get it over the threshold, prospects suddenly look much brighter because your ranking improves by an order of magnitude. Even then they may read a 0 (but a high zero!) or -- better yet -- a low 1.
It becomes a question of whether you are flagged as penalized or not. You cannot tell by merely reading a 0 on the toolbar. You need to analyze your history with Google, going back several months and several crawls. In my case, I don't think I was ever penalized. (Well, I got zapped once for duplicate doorway pages, and this kicked the pointed pages below the threshold, but the pointed pages themselves were not deliberately zapped. They merely inherited less PR, which was bloody all by itself!)
My big problem is that I have too many pages that need to share a PR 7 from the home page. My situation is very unusual; Google's algos are not scaled for sites like mine. I have to tinker a lot to optimize for Google. If you are actually penalized, then I have no idea what you can do.
I think directory structure is most relevant only when the toolbar is a "guess." You have to determine that the PR you see on the toolbar is not a guess for a page that has not yet been calculated.
