Personal Project Planner (PPP) was a research PIM prototype. It created a folder structure through writing a plan of a project in a word processor. Every item from a list turned into an appropriate (sub)folder based on bullets nesting. It also allowed having additional text under bullets, writing email form it, link web content, etc. It basically let user focus on the project steps, while the hierarchy of folders followed.
If you want to try PPP, it is available for downloading and installing on the Windows platforms as PlanZ. It is available here.
A (way way) less sophisticated software T2F allows to create a structure of multiple nested sub-folders by writing a text file and running the program.
I know, I know. It’s just a simple ‘mkdir -p’ (Linux) or ‘md’ (Windows) in front of every line behind a fancy button :). And it doesn’t save a lot of typing either. Although it might come in handy sometimes.