this is how I organize my project folders. I know it's not the most effective way of organizing the projects I want to do but it's working for now. And this is how I organize my reference images. It's a bit of a mess I know but maybe it will help.
Mudbox or Zbrush, these programs are on the top for movie and game industry, for organic and non-organic. I would say, choose Zbrush. http://www.pixologic.com/zbrush/