I'd imagine it's a combination of a ton of different software in their workflow.
And at higher levels of the 3D industry, it ultimately comes down to whatever the pro is comfortable with. So realistically, it's really anyone's guess what specifically they use.
You'll probably want to look into the following though.
A polymodeller: 3DS Max, or Maya will do fine
And that's just to start. You'll probably want to start looking into rendering engines and shit like that later. And that doesn't even begin to cover additional shit like plugins that no doubt Nintendo uses.
Basically, its a fucking career. You're not going to learn Nintendo level skills for fun on the side.