Once you've picked a root page and decided on www vs. non-www, make sure that all your links follow the same convention and point to the root page that you picked. Also, I would use a 301 redirect or rewrite so that your root page doesn't appear twice. For example, if you select http://www.yourdomain.com/ as your root page, then if a spider tries to fetch http://yourdomain.com/ (without the www), your web server should do a permanent (301) redirect to your root page at http://www.yourdomain.com/ [GoogleGuy's posts, WebmasterWorld]
URLに www を含むか含まないかはともかく、どちらかに決めたら、そうでないほうにアクセスされたときは301リダイレクト使ってくださいね、ということです。
