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I'd be interested in tools helping to organize thoughts and ideas, especially in a non-linear way (i.e. not as most existing note taking tools, working with lists and bullets, but rather as a post-it application). Ideally, something like the tool they use in Minority Reports would be cool (without the fancy-touch thingy), but an important point would be the ability to visually connect different ideas/notes together.

EDIT: Maybe to make things more explicit, I have a visual memory, and it helps me a lot having a graphical disposition to classify things (like important things at the top-right, urgent ones on the middle-left, etc). Basically, I'd like to find my messy desk on my screen :)

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  • 5
    org-mode is tough to beat if you already use emacs (or even if you don't)
    – Abe
    Commented Mar 20, 2012 at 5:35
  • Maybe you should look at trello.com but this is online only afaik. Windows has such a functionality by itself too (at least my win 8.1 here at work). (It's to be found under %windir%\system32\StikyNot.exe and called "sticky notes"). Edit: Oh I just saw you wanted to connect those post it like notes ... both of my mentioned programs can't do that. Sorry.
    – Aron_dc
    Commented Sep 29, 2015 at 7:27
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    While you ask for software, I'm going to suggest hardware: A pencil, a pack of index cards, and your hand. Cards in different colors can be helpful. Or different colored pencils. In other words, just use a portable version of your desk. You can then arrange the cards as you like later - and rearrange them. You can transfer them to software, but the cards themselves remain useful. It is easy to add and discard cards (psychologically nearly impossible to erase anything in a software solution). The cards can form lecture notes, etc. If asked, I can expand this to a full answer.
    – Buffy
    Commented Jul 10, 2018 at 14:51
  • @Buffy OP has deleted their account, so you can make it an answer as you wish. Anyway, what do you mean by "psychologically nearly impossible to erase anything in a software solution"?
    – Ooker
    Commented Jul 11, 2018 at 3:47
  • Maybe Obsidian? They describe it as a "knowledge base on top of a local folder of plain text Markdown files." Notes are local and yours, but you can also publish them such as here. Plus you get some interactive connectivity maps for free!
    – Roald
    Commented Oct 5, 2021 at 6:18

15 Answers 15

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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.

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    Its an awesome stuff for presentations (I used it a few times). However, does it really work for note-taking for oneself?
    – Piotr Migdal
    Commented Feb 15, 2012 at 21:13
  • Thanks, I'm not sure I would use for note taking, but I definitely have to try it for making presentations! It looks really cool, even though I guess one needs a bit of time to use correctly.
    – user102
    Commented Feb 15, 2012 at 21:18
  • yes, the first presentation took me a while. But I think after having delt with it for some hours, you can be very quick to take notes when you use the default set of containers and not draw your own stuff.
    – SwissCoder
    Commented Feb 15, 2012 at 21:35
  • accepted for Springpad, which is probably the closest to what I'm looking for. I guess I will have to code my own in order to be completely satisfied :)
    – user102
    Commented Feb 16, 2012 at 21:15
  • Prezi is great, but not technically non-linear- it requires that you specify a linear path
    – Abe
    Commented Mar 20, 2012 at 5:32
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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.

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    Yes, they are interesting, but somehow too complex to use, especially for longer thoughts. I just tried XMind, and I've tried SimpleMind before, and it seems to lack the ability to quickly write something down, and then to later one connect it to other things (at least in a simple way).
    – user102
    Commented Feb 15, 2012 at 17:10
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    I prefer FreeMind. It is a bit bloated but once you get to know the shortcuts, its as good as writing by hand.
    – user107
    Commented Feb 15, 2012 at 20:31
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    If you think FreeMind is bloated, you can recur to FeePlane
    – Open the way
    Commented Feb 26, 2012 at 8:01
  • @CharlesMorisset: in FreePlane and FreeMind (and probably XMind as well), you can move around a node (and all it's subnodes) by CTRL+arrow_keys. Or simply cut (ctrl+x) and paste it under the node where you want it. You can also go back/forth between nodes and regular *.txt files (it will lose formatting, but keeps the node branching intact. Note that some are annoying with URLs as they treat them differently, so exporting/reimporting make them visible twice). Usually, [Return] creates a node under the current one, and [Tab] create a "child node" underneath the current node. Ctrl+left moves up
    – Olivier Dulac
    Commented Sep 24, 2013 at 18:00
  • Another option is MindNode, which comes in both Free and Pro versions. I've found it very useful, and has support for on-the-fly writing, as well as outliner export.
    – Matthew G.
    Commented Nov 25, 2013 at 18:06
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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.

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  • I remember trying TiddlyWiki a while ago, and although I thought it was quite good, especially with the ability to use it with Dropbox, it doesn't seem that it's possible to organize in two dimensions the posts :(
    – user102
    Commented Feb 15, 2012 at 16:48
  • I use a MediaWiki as a personal wiki for a while now and I’m quite happy with it. The installation is quite sophisticated though (you will need a local webserver with PHP, a MySQL database and LaTeX).
    – Lenar Hoyt
    Commented Aug 17, 2013 at 0:16
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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.

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  • Exactly what I was looking for when arrived at this question.
    – Dan Oak
    Commented Nov 26, 2019 at 21:16
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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.

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  • Thanks for you answer, but do these wikis have a functional graphical interface? I'm really interested in something that can help me visually organize things, if I want to write notes down, I can use Latex directly.
    – user102
    Commented Feb 26, 2012 at 12:22
  • @CharlesMorisset the GUI is minimal, like text editors but with advanced options.
    – Approximist
    Commented Mar 9, 2012 at 0:11
  • @Approximist Check out github's wiki engine, gollum (gem install gollum is enough!). 1. Everything is stored as markdown files (no db), can be edited with your favorite text editor. 2. support latex equation by default via mathjax.
    – pcr
    Commented Mar 20, 2012 at 13:11
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    Zim is available cross platform at least since it was ported to python. For Windows a native installer is available, where it is compiled into an executable (which provides better integration with the Windows desktop than running a python script). The only downside is, that it sometimes suffers issues when renaming/moving pages, presumably due to the file-system differences (e.g. you cannot rename a file or folder, while any program has opened it even for reading or as working directory).
    – kdb
    Commented Sep 12, 2014 at 15:00
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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.

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  • Thanks, Scrivener looks really good, but indeed a bit too writing-oriented. I guess a mix between Scrivener, TiddlyWiki et a mind mapping tool would be perfect :)
    – user102
    Commented Feb 15, 2012 at 23:05
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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.

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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.

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  • Thanks for the link, I will check it out! The absence of support for equation editing might be a problem though, as I'm also using only Latex.
    – user102
    Commented Apr 18, 2012 at 22:01
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Here is another one, which I find very helpful and intuitive: CmapTools

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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.

enter image description here

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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

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The last answer to this ancient question is 3 years old, so let me add a more recent development. In the past few years, many excellent note-taking programs have become available that allow you to do this. This type of software is often branded as allowing you to "build a second brain". (I'm not particularly endorsing that kind of hype branding; just hoping to provide a useful search keyword.)

Conceptually, you may be interested to look into the Zettelkasten methodology. There, the idea is to have short, atomic notes on individual subjects that are extensively linked to each other. There is a large community around this.

In terms of specific software, recent popular non-linear note-taking competitors include Obsidian (which I personally have been using for a while now and think is excellent), Roam, LogSeq, and Scrintal.

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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.

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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!

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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
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