When comparing Zim 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 Zim is ranked 3rd. 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.
Specs
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Pros
Pro Allows for organized, wiki-style navigation
Notes can contain links to other notes, allowing you to reference important information when needed. This way the user can connect and reference many different pages in the app, keeping things clean and structured, unlike Evernote, which makes this a good Evernote alternative.
Pro Plain text data format rather than proprietary
If/when the app is no longer developed (or if the user simply decides to no longer use the application or view/edit it on a non-supported platform), this can still be done with any plain-text editor.
Pro Automatically manages files and folders
Zim will automatically create a folder structure that fits your page hierarchy and adds/removes files such as images to/from appropriate folders.
Pro Good export options
Zim supports HTML, LaTeX, Pandoc Markdown, and RST. This allows ones documents to be easily used in a wide selection of other apps.
Pro Support for multiple platforms
Windows, Linux, and BSD are supported with their own clients. This is nice for those that use multiple operating systems but still want to use the same app on each.
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 mobile app support
This is a desktop app and there are no mobile versions available. This can make it more difficult to use on-the-go if using cloud storage to store files from the app, as there is no mobile app version to access those files.
Con No native sync support
Zim notes don't automatically synchronize with other devices or offer built-in cloud sync support. Of course the user can add the files to Dropbox, or something similar, to then open them on another device with the app installed. But this is more of a work-around than a built-in solution.
Con Looks ancient
Zim has a very plain and outdated interface.
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.