Search Engine Friendly Design - Server Side Includes
Server side includes are perfectly fine to use as long as the end result is search engine friendly. In other words, if the page that the viewer sees is search engine friendly (text links, html text, etc) then there is no problem. SSI is not considered spam and will not harm a site's rankings as long as the end result is a search engine friendly page.
NEXT Step: Use a Robots.txt File