Is there any efficient non-linear note-taking software?
Mind maps might be what you're looking for.  From the Wikipedia page:


  A mind map is a diagram used to represent words, ideas, tasks, or other items linked to and arranged around a central key word or idea... Mind maps are used to generate, visualize, structure, and classify ideas, and as an aid to studying and organizing information, solving problems, making decisions, and writing.


There are lots of mind mapping tools out there.  I've used XMind before.  

One drawback is that it's hard to put longer thoughts into a mindmap.