What program does Square-Enix use to make their art?
Square Enix use numerous types of software to implicate their CGI and Game Design. Originaly, for the original Final Fantasy Games, they were written in the specific console propriety assebly code format.
Today however, is completely different as a few years ago they developed their own personal game engine called Crystal Tools (which is unavailable to the general public or other companies [Unless bought for several million pounds or more]).
When it comes to the CGI, they have used (not sure if they still do) Maya Software, which is one of the leading industry based animation software. There is also 3D Max Studio: each of which is incredibly expensive, yet well worth the purchase. For their actual concept designs and wallpapers, etc, I believe they use Photshop, Adobe After Effects and Illustrator; as these are the leading brands at the moment.
They also use a lot of DirectX within their CGI.