What flight simulator software did Captain Zaharie Ahmad Shah use?
Based on the red little strip (notification bar) on the bottom of the instrument panel in the middle, it must be either Microsoft Flight Simulator or Lockheed Martin Prepar3d. The red notifiation bar is specific to Flight Simulator 2004 (FS9) and Flight Simulator X (FSX). Laminar Research's X-Plane uses a different graphics engine and would not have produced a scenery that looks like on the three outside view screens.

The source is not really quotable, but if the name and picture can be taken a proof, then Mr Shah himself writes on the X-Sim.de Forum about FS9 and FSX being used:


  Elo guys,
  zaharie here.... pls to join x-sim. About a month ago I finish assembly of FSX and FS9 with
  6 monitors .... with the latest graphic card ( 2 pieces of asus 7970) on one cpu awesome view on 3 panasonic 32 in. LCD HDMI
  and 3 touchscreen Dell 21 inches for main (MCP) , center pedestal, overhead panel.
  time to take to the next level of simulation.Motion! looking for buddies to share this passion.
  Capt Zaharie Ahmad Shah
  BOEING 777 MALAYSIA AIRLINES


Answer based on own experience with all 3 simulators/publishers.