When comparing MDwiki vs iA Writer, the Slant community recommends iA Writer for most people. In the question“What is the best cross-platform note-taking app?” iA Writer is ranked 52nd while MDwiki is ranked 70th. The most important reason people chose iA Writer is:
The Noise Free Writing Experience is one of the first approaches to create a first class distraction-free environment. The feature hides the Mac program bar when you start writing.
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 Noise Free Writing Experience removes even the program bar
The Noise Free Writing Experience is one of the first approaches to create a first class distraction-free environment. The feature hides the Mac program bar when you start writing.
Pro A mode that brings focus to the sentence you're working on
Enabling Focus Mode will dim the whole text except the sentence you are currently writing on.
Pro Can tell how long it would take to read through what you've written
Pro Markdown support
Pro Syncs using iCloud and Dropbox
iA Writer can sync documents using iCloud or Dropbox from within the editor for use across multiple devices.
Pro Create whole document by including separate images/markdown docs
This is new and very awesome feature in iA Writer 4.0.
Pro Can export a Word document
Pro Available for all Apple devices
iA Writer is available for Mac, iPhone and iPad.
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 No Linux support
