Is there any efficient non-linear note-taking software?

Not recommending concrete programs, but tools that have quite a few implementations

Have a look for:

• Mindmaps
• Desktop Wikis or locally installed Wiki software
• Bugtracker
• For collaborations possibly forum software
• Kanban Software
• Other "Getting Things Done" (thats the name of a concept with many helpful tools) software
• Citation management Software
• Find a concept for organizing your files, such that you find them quickly. Possibly install an alternative file manager that is more intuitive for you

This question is quite old, but I'll mention a solution that has worked extremely well for me: the vector-graphics program Inkscape.

A new Inkscape document essentially acts like an infinitely-large piece of paper. It allows you to write notes with a pen via a touchscreen or external graphics tablet and also type text on a keyboard using the text tool, along with many of the other useful features of a vector graphics program (lines, boxes, colors, etc). You can easily move objects around and scale them infinitely. The file sizes are quite small, even for relatively large mind maps. You can copy and paste your calculations, drawings, etc.

Perhaps this solution is a bit unconventional, but I've been using it for the past 3 years as my main note-taking software for physics and mathematics research. Once you customize the program settings to your liking and perhaps add a few system hotkeys, it works very well!

I'm not sure how this old question got bumped back to the top, but I can offer an answer: TheBrain is a very nice dynamic concept map with a lot of sophisticated features. Unlike Scapple or some of the other suggestions here, it's currently under active development.

The downsides are that it's a little pricey (but they offer academic discounts if you contact them) and it doesn't have equation editing, although there are workarounds for that.

TiddlyMap.org - I just found it after looking at your question... Searching through another site.

It works with TiddlyWiki - the recently developed version.

TiddlyMap will let you make a clickable graph of your wiki tiddlers, and show you real time navigation as well of where you are in your graph.

http://www.revolvy.com/main/index.php?s=TiddlyMap

DenkWerkZeug - http://denkwerkzeug.com is an application I have been looking at for a while and learning about. It combines a Wiki with a graph and semantic principles, but is not difficult to learn, a fascinating application.

And one more named Vis-a-Wiki, that I have heard about that combines a visual approach with wiki and graph as well as Scrumban board... Vis-a-Wiki has 'context sensitive navigation'.

I include these together not take away from, but hope as to just let people know about the existence of these independent software projects.

http://marko-editor.com/vis-a-wiki/

Hope this helps... -jariell

Although the question is old, my answer may benefit future readers.

I've recently started to use Gingko App. You can hierarchically organize your notes, which are themselves written in card-like units. The possibilities are many, depending on your organizational creativity. For long-form note-taking this is better than mind maps, while providing all many of the benefits of mind-mapping.

Since you are asking here, I assume note taking for paper is important. Docear is a mind mapping for paper tool which based on Freeplane and Jabref, which might fit academia needs perfectly. And it supports windows, linux and mac. And it' s GPL licensed.

I use scapple from https://www.literatureandlatte.com/scapple.php

It does exactly what you want. You can put notes anywhere on a canvas. You can connect them if you want. And you can search them.

It costs about $15 and there is a trial for 1 month so you can see if you like it before you buy it.

It works very well if you use the Crawford slip method of brainstorming.

It's one of the best piece of software I use.

Here is another one, which I find very helpful and intuitive: CmapTools

A nice tool I have found for this is Visual Understanding Environment (VUE), which is an open source tool that sounds very much like what you are looking for. You can position nodes how you like and sketch connections between them. It even has a nice mechanism for nonlinear presentations by setting pathways between the elements in your file. The presentation mechanism is not as polished as Prezi, but since you are looking at note-taking rather than presenting, this should not be an issue.

The only thing keeping me from using it more is that there currently is no support for equation editing, LaTeX or otherwise, which is a deal-breaker in my field. There are workarounds like using Laeqed to generate PNGs of your equations, but it can be cumbersome for large projects. If this is not a concern in your area, I would recommend giving it a look.

I needed the same functionality for myself. I was looking for a powerful note-taking system and after considerable search concluded that the wiki format was best for dynamic unpublished notes and scribblings. I started by using desktop applications but needed some way to render math better so I shifted to web applications (running them locally you'll need an XAMP server).

Desktop Applications

Zim Desktop Wiki - A wiki notebook. Really good imo.

WikidPad - Described as an IDE for your thoughts. Offers same functionality.

Server Based

Mediawiki - If you're going to end up with thousands of documents being edited by thousands of users then it is the best. For personal use it is a bit of an overkill, and the spaghetti php code doesnt help.

Instiki - currently using this. Compact and simple. You can easily back it up to an USB disk. Or export all pages to html. Needs ruby to compile though.

A couple of other options for mind-mapping software:

I tried using Curio, which is a very powerful program that can do mind-mapping, as well as a whole lot of other activities. The problem I had with it was that it was, if anything, too stuffed with features: I couldn't really figure out how to get simple tasks done, because there was so much work to do just to learn how to do anything at all. However, I'm certain you wouldn't run out of features.

If what you're looking for is something a little less complicated, but still in the sense of mind-mapping, you can try something like OmniGraffle Professional, which produces diagrams and organizational charts of almost any shape or complexity. It doesn't try to be the "all things to all people" that Curio is.

Another "out of the box" solution is Scrivener, which might be a little too text-based for your needs, but is a great tool for writers.

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.

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.