I just noticed something that might be worth putting in this codex page, but perhaps others ought to confirm it first.
I'm using the standard permalinks and all my posts and pages have the same PageRank (5) as my main page. I checked another site with the same PageRank (5) on the front page that is using custom permalinks and other than the front page all the pages had a PR of zero. I'm just theorizing here, but it appears that for PR purposes http://www.tom-hanna.org/ and http://www.tom-hanna.org/?p=772 are reading as the same page.
For what it's worth the categories on my site, where the URL is something like http://www.tom-hanna.org/index.php?cat=15, are all showing up as unranked.
Anyway, it looks as if for sites that have a lot of incoming links to the main page, the custom permalinks could actually backfire search engine wise.
Just food for thought. Might be worth looking at this across several blogs and seeing if it holds up.