In the eyes of the search engines httm://www.mysite.com is not the same as http://mysite.com even though for most people it will be the same site, the same information tends to be displayed.

However as the search engines see these as different pages with the same information on you run the risk of getting flagged for duplicate content, also if some one links to your site and uses the http://mysite.com verson of the link rather than the http://www.mysite.com then the search engines may confuse where to credit with the link.

With sites that have hundreds or thousand of pages this can become a nightmare to organise and keep control of, however there is now a new element that the search engines have agreed to respect that should help solve this problem it is the canonical element.