Authentication system

I am in the process of scripting a site which requires authentication. I've no problems with the scripts allowing folk to register, login, logout, change password, etc. However, this morning I've begun to work on providing some "security" in the form of preventing someone from registering as another person. This site will be limited to those who are members of a particular electronic (religious) community. I want to be able to verify that the person registering as "George Fox", for instance, is George Fox. At the point where they fill out the registration form, I am sending them an email, informing them that they have been registered. On many sites I've gone to, the process then includes a requirement that the person reply to the message. Now I need to learn how to take the incoming message and process it. I am assuming that the processing can be done by php. Any suggestions, either on how to do this, or where I might learn how to do this? Doug