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Set wcf service credentials in config file for a service with endpoints created in code
var svc = new ServiceHost( typeof (MyService), new Uri(s));
svc.Authorization.PrincipalPermissionMode =
                  PrincipalPermissionMode.UseWindowsGroups;
svc.AddServiceEndpoint(typeof(IMyService), new WSHttpBinding("MyBinding"), "");
//svc.Credentials.ServiceCertificate.SetCertificate(
//    StoreLocation.LocalMachine,
//    StoreName.My,
//    X509FindType.FindBySubjectName,
//    "mycertname"
//    );

<system.serviceModel>
     <services>
       <service name="MyNamespace.MyService" behaviorConfiguration="MyBehavior">
       </service>
    </services>
    <bindings>
      <wsHttpBinding>
        <binding name="MyBinding">
          <security mode="Transport">
            <transport clientCredentialType="Windows"/>
          </security>
          <!-- Or for message level security
          <security mode="Message">
            <message clientCredentialType="Certificate"/>
          </security>
          -->
        </binding>
      </wsHttpBinding>
    </bindings>
  </system.serviceModel>

<behaviors>
      <serviceBehaviors>
        <behavior>
          <serviceCredentials>
            <serviceCertificate findValue="mycertname"
                                x509FindType="FindBySubjectName"
                                storeLocation="LocalMachine"
                                storeName="My"/>
          </serviceCredentials>
        </behavior>
      </serviceBehaviors>
</behaviors>