When comparing MindMeister vs Org-mode, the Slant community recommends Org-mode for most people. In the question“What is the best cross-platform note-taking app?” Org-mode is ranked 1st while MindMeister is ranked 33rd. The most important reason people chose Org-mode is:
Org-mode is characterized by a flexible and versatile system with adaptability to different workflows, making it comparable as an Evernote alternative. It is at once simple and complex., which helps it to compete as an Evernote alternative.
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Pros
Pro Web and mobile versions available
In addition to web software, MindMeister is available on iOS and Android mobile platforms as well.
Pro Notes can be shared and collaborated on in real-time
MindMeister allows sharing maps with an unlimited number of collaborators so it's possible to take notes and brainstorm together. Mind maps can be shared by inviting people either directly via email or by sending them a link to the map. Even people without a MindMeister account can access the maps and even edit them.
Pro Comments and votes
Users can create polls and have collaborators vote individual topics up or down, or comment on them.
Pro Various layouts
User can switch between classical mind map layout, a layout where all topics are aligned on the left or the right, and org chart layout.
Pro Clear overview without losing any details
The mind mapping format provides with a clear overview of connections, hierarchies and relationships of notes. At the same time, it's possible to add more detailed notes, links, pictures and even whole files to the keywords, so that no important information gets lost.
Pro One node can have marks, emoticons and comments
Pro Adding a Table or Matrix
Xmind is one of the few mind maps that allows you to add a table or matrix to your mind map. Very useful when you have content that works better in a table.
Pro Very flexible
Org-mode is characterized by a flexible and versatile system with adaptability to different workflows, making it comparable as an Evernote alternative. It is at once simple and complex., which helps it to compete as an Evernote alternative.
Pro Built-in agenda
Org-mode has some built-in agenda functionality. You can schedule tasks and assign various degrees of importance to each of them. Org-mode agenda can also be synced with Google Calendar.
Pro Versioning can be tracked and synced using Git or other VCS
Org files are plain text, and lend themselves well to version control. Emacs also has good integrations for various VCS.
Pro Great sync support
Notes and to-dos can be synced with Trello, Toodledo, Simplenote, Orgmobile, or with tools like Git on Github, Dropbox, Google Drive, and Bitbucket, while WebDAV (with iOS and Android) can also be exported to PDF, mind map, LaTeX, HTML, Docbook, or txt.
Pro Basic spreadsheet functionality
Org-mode has some basic spreadsheet functionality. Other than auto-formatting ASCII tables (a notoriously annoying problem), it also has support for LISP-like syntax to define equations or any other functionality that can be achieved through spreadsheets.
Pro Out-of-the-box Latex support
Org-mode has out-of-the-box support for Latex: it can immediately parse equations (or other Latex markup) and can even compile notes to PDF or HTML.
Cons
Con No good offline mode
You can only work completely offline when using an iOS or Android device. For your browser there's only a clumsy 'offline mode' available. If you didn't hit the switch before you have the need for working offline (for instance: in a meeting, at a customer's location, in a plane, etc.) than your out of luck... no tool for note taking. Especially with all those HTML5-capable browsers and the Chrome App store (including Desktop apps), this limits the usage of this commercial product.
Con Expensive compared to the competition
A basic monthly subscription ($92 USD) gives you no more than XMind FREE except PDF exporting. XMind paid with PDF export is $79. $20 less for lifetime use of an app with more features as of writing.
Con Free option limited to 3 mind maps
A free XMind app/online account or MindMup account both provide unlimited mind maps.
Con MindMeister has very poor Evernote integration
Evernote is the number one 'store-everything-archive' when it comes to unstructured data or information. MindMeister markets there Evernote integration as a very cool feature. But this integration is very basic and buggy: only the last 50 (?) notes from Evernote's default notebook are shown in the list, and it takes about 30 seconds to one full minute to generate that list. After that it takes about the same amount of time to add a copy of the selected note as an attachment to a topic. MindMeister support is well aware of this poor implementation, but doesn't put any effort in fixing it.
Con Very basic
Con The interface has only very basic features
For example, it lacks the possibility to define a long text under the node title showing it in a permanent way. The software is 1000 less powerful than Microsoft Visio. Meanwhile it should just be more specific.
Con Difficult to learn
Org-mode has a difficult learning curve since you have to learn all the keybindings and commands. It's especially difficult if you are not used to Emacs.