I’m not sure if this has been mentioned, but last week the big 3 search engines finally agreed on a new link element to clean up most duplicate content once and for all (theoretically). Basically, what this means is you can stick a tag such as:
<link rel="canonical" value="http://www.example.com/index.php/template_group/template/{url_title}/"/>—or however you choose to handle it—in your header templates and they will index your site properly regardless of how people choose to link to you.
Read more about it from Matt Cutts (Google web spam guy).