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.

For non-linear note-taking and also collaboration I use TiddlyWiki. It is one file that stores all your notes as an interactive wiki. Through a plug-in it support LaTeX-math. If you throw it on a shared dropbox then it can even be a quick way to share ideas with colleagues. If you want something more formal than dropbox, then there are hosted options like TiddlySpace.

For nice graphical note editing/drawing:

If you get the hang on it, you probably could use http://prezi.com/

Your notes would look great, and you can always zoom in and out, if you want to add details.