In ASP.NET 2.0 Beta 2, two new configuration classes have been added:

1- ConfigurationManager:
     Used to update sections inside the App.Config file.

2- WebConfigurationManager:
    Used to update setions inside Web.Config file.

To see how to add some keys to the AppSettings section in the web.config file, check the code below:

Configuration configFile = 
                  WebConfigurationManager.OpenWebConfiguration("~");
AppSettingsSection AppSection = 
                  configFile.GetSection("appSettings") as AppSettingsSection;
AppSection.Settings.Add(
                 new KeyValueConfigurationElement("SMTP", "mail.bhaidar.net")
                       );    
configFile.Save();

The above code would add the following line to the appSettings section.

<appSettings>
    <add key="SMTP" value="mail.bhaidar.net" />
</appSettings>

Make sure to include:

using System.Web.Configuration;

Hope that helps you.

Regards