Does anyone know what software they used to make appleseed?

“SOFTIMAGE|XSI” I believe.

Is there a specific reason XSI seems to be used a lot in Anime?

I didn’t know it was. The only thing that I know of (anime-related) is appleseed.

What else was XSI used for?

Well studio Ghibli uses it for all the 3D elements of their moves. It’s also used a lot more for animation in Japanese games the way that Max is used in america.