As far as "
SEO" (in quotes because I am not really sure it falls under that category) I have seen bots from smaller engines choke on links because of the base tag. Typically, this tag is intended for use in large scale corporate sites where a section might be moved around so a single change to the page could keep all the links on the page relevant, but now there are better back-end tools for managing this, so the base tag will possibly be deprecated soon. In any case, as previously mentioned, it is not getting much use anymore.