When comparing MDwiki 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 MDwiki is ranked 70th. 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 Possibly more secure on web server
Due to the lack of a built-in editor MDwiki may be less susceptible to spam and defacement compared to other options when served from a web server.
Pro Doesn't require a web server
MDwiki is a self-contained JavaScript app that is very fast and can run in some web browsers such as Mozilla Firefox.
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 External program must be used for editing
A separate program must be used to make changes to documents as MDwiki lacks a built-in editor.
Con Requires additional permissions in Google Chrome
Supposedly, you can get it to work in Google Chrome by modifying JavaScript permissions, but these same changes may decrease security.
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.
