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The search engines do not see the include method, they only see the finished output with the included content already in place. So the method you use to execute the include has no effect on search engines. What does have an effect is the CONTENT of what you include - the included document. That content needs to follow all the best practice for SEO that you can drum up - plus the final output should validate:
W3C Validator - HTML [validator.w3.org]
W3C Validator - CSS [jigsaw.w3.org]