We are both attacking this from different angles. 

I created a simple page I call siteindex.  It is just a listing of all the stories on the site with direct links to them.  I created this because I noticed that Google almost always had a link only to index.php.  We all know that on a good site this changes all the time.  What I wanted was for google to index the stories using the actual link to the story.  It worked.  Google picked up the site index and the actual stories themselves have started showing up in googles index.  Here is the page siteindex.php that you can place on your site.  Somewhere on the front page make a link to it.  It can even be in the footer -- its meant for Google not your normal visitors.

Vinny developed a way to use apache rewrite rules and the geeklog url rewrite routine to make a search engine friendly direct link to the stories.  The hope here is that search engines that will not follow links like index.php?story=99234234 will follow these links and index the stories.  These search engines are not as quick as google to index sites and we anticipate this will take at least a month to see if it works.  Stay tuned for the results of this experiment.  You can see this in action in with the (Permanant Link) on all the stories here.

If this works as expected, Vinny and I will be releasing a package containing both hacks, that should solve most search engine woes.

TomW