It doesnt so much matter if you have the content in directories or not from and SEO perspective, from what I have experienced.
The key is getting the index page of those folders linked from your main page, and having all the links withing that folder linked from that folder's index page.
That keeps everything no more than 3 levels deep. home page ->first click(subfolder)->final content.
Do that, and get your homepage at a PR5 or above. PR6 actually seems to get you deep content indexed even better by google.
If you have more than one domain name, make sure they all redirect to one domain. In addition, make sure you redirect to http://www or http://domain. Doesn't matter which you go for, but make sure all your traffic redirects to one or the other.
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