My rule of thumb is to pick a root page and be as consistent as possible. I lean toward choosing http://www.yourdomain.com/ but that's just me; http://yourdomain.com/ would work as well. Then I recommend that you make things as simple as possible for spiders. I recommend absolute links instead of relative links, because there's less chance for a spider (not just Google, but any spider) to get confused. In the same fashion, I would try to be consistent on your internal linking. 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/

So the high-order bits to bear in mind are
- make it as easy as possible for search engines and spiders; save calculation by giving absolute instead of relative links.
- be consistent. Make a decision on www vs. non-www and follow the same convention consistently for all the links on your site. Use permanent redirects to keep spiders fetching the correct page.