It depends on whether the setting you have chosen is at "User" scope or "Application" scope.

User scope

User scope settings are stored in

C:\Documents and Settings\ **username** \Local Settings\Application Data\ **ApplicationName**

You can read/write them at runtime.

For Vista and Windows 7, folder is

C:\Users\ **username** \AppData\Local\ **ApplicationName**

or

C:\Users\ **username** \AppData\Roaming\ **ApplicationName**

Application scope

Application scope settings are saved in AppName.exe.config and they are readonly at runtime.