I never actually thought of the tracking ramifications before, but occasionally I work with sites that have both the www. and non-www. versions of the site live. Does this interfere with tracking in Google Analytics? (i.e. would I see double stats if someone visited domain.com/product/ and another user visted www.domain.com/product/)
As a side note, I know that you can now verify Google Webmaster Tools via Analytics if you already have it implemented, and you can set the preferred domain to either www. or non-www. in Google Webmaster Tools. So...maybe that takes care of it?