According to the GoogleGuy, the best way you can ensure that search engine spiders get your sites content as expected, you should use absolute links rather then relative (meaning to use the full web address, including your domain name instead of just the pages file name and relative position) in your site menus. The downside of absolute links rather then relative is that your site is then less portable, but if that portability comes at the expense of search engine ranking then it’s probably not worth it.
Also of interest is the suggestion that if your site resolves with both www.example.com and just example.com you should choose one or the other and use a 301 (permanent) redirect to direct all requests to the chosen one. The main reason for that is probably to ensure your site is not penalised for duplicate content but it’s a good idea anyway, particularly if you use cookies on your site.