I have actually recently started using Vim with folding (set shiftwidth=2, set foldmethod=indent) for my nested todo list and also note-taking. I have a single file with the following items:

  Work
    Topic 0 (work-related)
    ...
  Personal
  Tasks
    Ongoing
      ...
    Completed
      2012-08-22
      ...
    Future
      2012-08-23
      ...

One thing I like is that it's trivial to make subitems of an existing item. I often end up taking notes (such as URLs of consoles or associated bug IDs) under tasks listed in "Ongoing", which I think saves me a bit of time.

Anyway, while there are some things I still need to tweak, I am, overall, quite happy with the workflow it allows and so just figured I'd share this in case it helps someone else.