The search engines see's what code is on your page when you upload it to the server, not what you see when you View source on the page from the web.
If you code is all includes, you have no chance of ranking that site unless you can plug in some static content, either hidden in code or visible on the actual page.
Trust me I know, I've been battling it out with a Cold Fusion site that is 100% includes and html content plugins where the only pages I can get ranked are the static promotional pages. What you see from the web has no bearing on what the SE see's. An example is
http://SmutDrs.com - every peice of code on that site is from an include. Not one bit of static content. Can you tell? Only the webmaster truly knows.
SE's cannot spider or index included content yet. They are just now becoming able to spider and index flash movies however
Google can do links and AllTheWeb.com and indes links and actual text in the flash movie
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