Rhinoceros + Grasshopper with Lunchbox and Weaverbird plug-ins opens up some incredible opportunities for shoe design.
Autodesk Within is another application creating optimized generative structures. It was used by Under Armour for their Architech 3D printed shoe. Autodesk’s Shoemaker Pro and other footwear design software have been discontinued.
iCad 3D+ is a 3D modeling environment geared especially towards footwear and outputs STL and IGES formats.