I was wondering if you know anything about the www prefix. My hosting company has my site registered with the www and without, as the same for all sites, I believe. Does this affect how the websites are viewed by the search engines? Also, some directories have my site listed without the www even if I have submitted it with. Does this affect how Google for example counts external links to my site? I have asked many people and no one has been able to answer my question.
Timely question! I was just discussing this issue today on Twitter. Just to clarify, when you talk about your site being listed with and without the www prefix, that’s called the canonicalization of your domain. Basically, it just refers to your preferred URL for a site, whether that’s with the www prefix or without. Matt Cutts goes into more detail about canonicalization in this post.
Search engines can sometimes index both versions of your domain, creating duplicate content headaches for you and also link popularity dilution. For those reasons, I strongly recommend you decide which URL version you are happiest with and implement 301 permanent redirects at the server end to ensure your preferred version is served no matter which version is typed in. You can also set your preferred domain within Google Webmaster Tools.
Loren Baker wrote a post about the canonicalization issue today, so you might find that helpful. I concur with Loren that using the www is a no-brainer.