When comparing MindMup vs StackEdit, the Slant community recommends MindMup for most people. In the question“What is the best cross-platform note-taking app?” MindMup is ranked 17th while StackEdit is ranked 28th. The most important reason people chose MindMup is:
MindMup allows focusing on thoughts and productively capture them without getting in the way.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro Frictionless interface
MindMup allows focusing on thoughts and productively capture them without getting in the way.
Pro Browser-based
Don't need to install anything, just open the website and you are set.
Pro Just works
Pro Compatible with Google Drive and Github
Pro Easy sharing & presenting
After taking notes, it only takes seconds to share and/or prepare them for presentations.
Pro Free and open source
MindMup is free with source code available on GitHub.
Pro Works online and offline
StackEdit works within your browser. You need internet access to connect to the website, but once it's loaded, the site does not require an internet connection - you will be able to edit and save files locally. Additionally, you can use Fluid to turn it into a native desktop application.
Pro Supports various Markdown flavors
Supports standard Markdown and Markdown Extra.

Pro Simple workflow
It is very easy to toggle between the preview and the editing windows. The black makes it a very focused writing environment. Of course it's possible to change that if needed.

Pro Great when in full-screen
Pro No need to install additional software
StackEdit works directly from the browser, there's no need to install additional software as long as you have a web browser installed on your computer.
Pro Real-time preview
The preview shows in a collapsible pane on the right hand side.
Pro Instant publishing
StackEdit allows pushing a document directly to a list of publishing or file storage platforms or any SSH server.
Pro Multiple export options
Can export to .txt, .html and .pdf.
Pro Syncs via Dropbox and Drive
Files can be synchronized through Dropbox and Drive.
Cons
Con Note capacity is limited
MindMup is good for mapping out thoughts that could be summarized in bullet points, but longer notes aren't as practical for this service.
Con Unconventional note taking style
It's a mind mapping application, not a traditional text based note storage platform.
Con Saves files in browser's local storage
Local storage is limited and if the browser crashes the text can be lost.
Con Cannot be accessed while being offline
Even though the editor itself works offline, you need internet access to open the website and the editor.
Con Lacks a good integrated spell checker
Uses the built-in browser spell checker which may not be as good as spell checkers other editors have. Depending on the browser, of course.
Con Publishing to GitHub requires giving write access to repos
In order to publish documents to GitHub, StackEdit requires writing access to your repos, something which many people may not be comfortable with.
