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.