When comparing Zim vs Org mode for Emacs, the Slant community recommends Org mode for Emacs for most people. In the question“What are the best knowledge base systems for personal use?” Org mode for Emacs is ranked 3rd while Zim is ranked 7th. The most important reason people chose Org mode for Emacs is:
Org mode started out as a simple outlining/note taking app. Then each outline heading can optionally be a TODO list item. And if you desire, you can add SCHEDULE and DEADLINE dates. (Schedule being the date you'd like to start the item.) You can customize the TODO states to add things like DELEGATED, WAITING, BLOCKED, etc.
Specs
Ranked in these QuestionsQuestion Ranking
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 Can be as simple or as complex as you want
Org mode started out as a simple outlining/note taking app. Then each outline heading can optionally be a TODO list item. And if you desire, you can add SCHEDULE and DEADLINE dates. (Schedule being the date you'd like to start the item.) You can customize the TODO states to add things like DELEGATED, WAITING, BLOCKED, etc.
Pro Libre/open source
Pro Cross platform
Emacs runs on all platforms, Windows, Linux, OSX, even Android and IOS

Pro Exports data to PDF, LaTeX, HMTL and other
You can even build presentation or blog from your data

Pro Supports tables with formules (quite powerful!)
Pro Plain text data storage
Future-proof.
Pro Inline image displaying
Pro Free but copyrighted
Pro Fast interaction
Once muscle-memory sets in, can be much faster to use than a point & click program.
Pro Uses Emacs
Pro All apps
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 Obtuse documentation
The documentation assumes a level of understanding of basic Emacs usage that not all users may have.
Con Complicated to get started
Con Difficult to use as a database
For example, if you need to quickly populate client details on quotes, unfortunately its easier to find, copy & paste.
Con Not suitable for normal users
Not even a majority of software developers can be bothered to use Emacs (or VI, for that matter).
Con PDF export can be difficult
Latex assumes you're a (compliant) student, have to do a lot of research to get what you want out of it.
Con Uses Emacs (for those who prefer vi, menus, etc.)
