Joseph,
From what I gather, it's not the fact that a site is database driven, or not, that effects the indexing of a site. It's a matter of how many variables you are passing in the querystring as well as optimization. I don't think that search engines can differentiate between static and database-driven content since database-driven content is generated at the server.
I would be very surprised if large sites, such as Amazon and Microsoft, were static Web sites.
The way I have set up my site, in ASP, is that I have an administration for the services, products, links and portfolio sections. When, for an example, I add a service, it will take the title that I enter for that service, parse out all unnecessary characters to create a file name (e.g. the title Flash Design would be parsed out to something like flash_design_110.asp, the 110 being the record ID) and then create that file on the server using templates I have in place. When creating the file on the server, I embed the record ID at the top of the file as an ASP variable. By doing so, I no longer have to use querystrings in most circumstances.
I'm not all to familiar with PHP but you can rename files dynamically using, I believe, ModRewrite, or something of that nature. You could probably also do the same with PHP as I've done with my site if you like having physical files on the server.
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