When comparing Emacs Org-mode vs Moo.do, the Slant community recommends Emacs Org-mode for most people. In the question“What are the best cross-platform task apps?” Emacs Org-mode is ranked 3rd while Moo.do is ranked 11th. The most important reason people chose Emacs Org-mode is:
This app's flexibility is based on its minimalist approach, giving the user near-infinite freedom.
Specs
Ranked in these QuestionsQuestion Ranking
Pros

Pro Ultimate flexibility
This app's flexibility is based on its minimalist approach, giving the user near-infinite freedom.
Pro Absolutely free
Emacs with Org-mode is free as in beer and free as in speech – that is, it costs nothing and it’s totally open source.

Pro Files are usable anywhere at anytime
Users are not tied to one service provider, program, platform, or database engine.

Pro Incredibly extensible
There are many plug-ins for Org-mode, including Org-habits and Org-notify. If Org-mode lacks some piece of functionality, it is very easy to add it.
Pro Agenda views
Pro Excellent unofficial Android app (orgzly)

Pro Offline support
Pro Efficient features for deadline organization
Pro Supports plaintext spreadsheets
Pro There are a lot of extensions, for exporting to html, bootstrap, js-reveal and much more
Pro Quickly add rich text
Pro Agenda panel lets you see all your tasks
You can use tags like @next, @today, @tomorrow, and you will see all your tasks in agenda panel.
Pro Offline editor
Pro Very easy to get started with
Despite having many different features, Moo.do is extremely intuitive to use right from the start.
Pro Indefinitely nested lists of items
There is no limit to how many nested lists you can create. This gives you a lot of freedom structuring your ideas.
Pro Actively being developed
Pro Lets you view multiple panes
The multi-pane feature allows you to view lots of information on the same screen so there is no need to frequently switch between pages.
Pro Very fast to use
Very fast application which is useful when you want to brainstorm. No lags at all.
Pro Kanban
Kanban boards.
Pro Markdown
Markdown support.
Pro Multiple priority levels
You can quickly tag any of your content with one of the priority levels to help you stay organized and address the most important tasks first.
Pro Three different themes to choose from
You have three options (classic, outliner, and dark) for themes. The differences are specific to how your content is formatted (for example: how bullets are displayed, if at all). You can also toggle the "grayscale" option if you don't want your tags to be in color.
Pro Well designed interface
The design of the interface was well thought out. Despite the abundance of features, the interface is intuitive to navigate. It has a very clean, minimal design.
Pro Easily filter data using tags
You can #tag words anywhere throughout your notes in order to easily find them and keep similar notes organized.
Pro Turn your email into a todo list
Moo.do has an application for gmail that lets you fully organize your emails and turn them into a todo list. E-mails can be organized into different folders including what needs a reply, the priority levels, what is completed etc.
Pro Ability to zoom in/focus on a branch
Pro No limit on list items in the free version
Cons
Con Unintuitive user interface
The key combinations are unintuitive and difficult to remember. This is probably because there are a lot of hidden "modes" depending on where the cursor is. Actions aren't paired with reversing actions like in other todo apps. For example, hitting shift-tab does NOT reverse the effect of hitting tab.


Con Android app isn't very good
There are several user-created apps for Android, but none seem to offer the same level of functionality as other to-do apps.
Con Not really cross platform
Although it is possible to get a lot of it working, no all in one, sync included, out of the box solution is available for mobile devices.
Con By default, a hard-to-read display
The default way of writing an outline or checklist creates a very messy wall of text that's difficult to read with no vertical spacing. You can manually add vertical spacing, but the Org operations don't preserve it. There are pretty-display modes, but you need to remember how to enable them, etc. etc.
Con Interface can feel distracting
Moo.do offers a variety of features that can make for a distracted experience. Rather than being encouraged to focus on the task at hand, you may find yourself tempted to flip through other panes.
Con Undo / redo
Undo / redo can be buggy.
Con No API
Con No wiki-style cross references
Con Inability to add images to the outline
This is now possible
Con Currently lacks notifications for changes in panes
