It's fairly simple to change the Domino domain name. For the most part, that is just the domain name field in the server document, and the Domino Domain field in workstation location documents.
However, do you additionally want to change the organization name (certifier)? These are two different things. Domain is the @Company you see in internal email, while organization is the /Company you see in ACLs and various other places. Domain has to do wih mail routing, whereas organization has to do with security.
If you also want to change the /Company, that is a more involved process:
http://www-01.ibm.com/support/docview.wss?rs=463&context=SSKTMJ&context=SSPQ69&context=SSKTWP&context=SSRNU3&context=SSRNUY&q1=change+organization+name&uid=swg21088125&loc=en_US&cs=utf-8&lang=enYou said you wanted to