It depends on whether the setting you have chosen is at "User" scope or "Application" 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**
C:\Users\ **username** \AppData\Roaming\ **ApplicationName**
Application scope settings are saved in
AppName.exe.config and they are readonly at runtime.