When comparing Emacs Org-mode vs Omnifocus, 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 Omnifocus is ranked 63rd. 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
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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 Defer date
Omnifocus allows users to setup the "defer date" which can be treated as "start date". Tasks will not be marked as available until that date, which should help to focus on the "available" task only.
Pro Forecast summary
The forecast summary shows a quick digest of the tasks you have for the day. You can select any day to quickly see what tasks you have planned that day. For extra functionality you can connect with the iPhone’s Calender app, which allows you to also see any other events you have planned that day.
Pro See an overview of all tasks via "Perspective"
The Perspective section allows you to see an overview of the tasks you have set. It also allows you to set contexts or see things you have flagged.
Pro Nearby and context-sensitive tasks
OmniFocus 2 allows you to set up contexts for tasks in certain areas. This makes sure you never miss a task when you're out running errands and happen to be near something you need to do.
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 Mac and iOS only
Omnifocus doesn’t work on non-Apple platforms.
