No, they don't. Supreme Commander and its expansion are in the "Games for Windows" thing and they don't support the 360 controller natively.
So, GFW games that support gamepads must support the 360 controller and those that do must also document gamepad support by using the 'Xbox 360 names' (that probably includes images). Games that don't support gamepads at all aren't subject to these requirements.Games for Windows: Technical Requirements said:Games that support gamepad controllers must support the Xbox 360 Controller for Windows using the XInput API. If DirectInput peripherals are also supported, then DirectInput can also be used. However, XInput must be the default API if an Xbox 360 compatible device is used.
All references to common controller triggers and buttons must use the Xbox 360 names. See the Xbox 360 Common Controller for Windows Terminology list for details.
This thread fails, by the way