At the West Ohio Conference, we use Drupal as our Content Management System (CMS) for all of our sites, including all 8 district sites, West Ohio Camps and Imagine No Malaria. Drupal is an open source and very powerful CMS. You can find out more about Drupal at Drupal.com, including downloading it. It's free to download, but you may need some expert help to take full advantage of the software.
United Methodist Communications has some excellent resources for churches in the process of starting a web ministry or advancing an existing one. Here are the direct links to the pages on their website relating to church websites.