When comparing Org-mode vs Apple Notes, 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 Apple Notes is ranked 18th. 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 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.
Pro Sync with other Apple devices via iCloud, other cloud/email services
It syncs with iCloud, and surprisingly, also with Gmail and possibly other services too.
Pro Built-in
It's a default system app, making it easy to find and use since it is already installed.
Pro Rich-text editing
Allows for simple text formatting and making TODO lists with checkboxes.
Pro Attachments
You can add files to notes and then filter notes by attachment types.
Pro Supports sharing
Pro It's fast, and syncing is very dependable
The app launches quickly on both Mac and iOS, it also syncs quickly (in seconds) and very dependably across different Apple devices.
Pro It remains simple to use with a gentle learning curve
Despite the significant new updates in iOS 9 and iOS 10, you can start using Notes immediately, then try/master new features with ease — definitely a gentle learning curve.
Cons
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.
Con Cannot export to a format that can be imported again
This makes it obscure and cumbersome to back up your notes as files that could be managed by your backup system. You can export to PDF, but not in bulk; and this isn't the native format that you can easily recover with.
Apple compounds the problem by using some undocumented format for notes. You can, however, back them all up by backing up the files found in ~/Library/Containers/com.apple.Notes/Data/Library/Notes