When comparing MarkdownPad vs Smartdown, the Slant community recommends Smartdown for most people. In the question“What are the best open source Markdown editors for UNIX-like systems?” Smartdown is ranked 33rd while MarkdownPad is ranked 36th. The most important reason people chose Smartdown is:
You can add directories to the sidebar. These directories can be from cloud services (like Dropbox for example).
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Pros
Pro Allows customizing output
A custom CSS can be added to the rendered HTML to change the preview and output.

Pro Real-time HTML Preview
MarkdownPad is split in two panes. One pane is used for writing Markdown, the other shows the rendered HTML as it's written.
Pro Integrated file library
You can add directories to the sidebar. These directories can be from cloud services (like Dropbox for example).
Pro Advanced Markdown support
Smartdown supports Critic Markup and MultiMarkdown flavors of Markdown that add advanced functionality, like tables, footnotes, etc.
Pro Customizable
The app can be themed and the layout can be changed around.
Cons

Con Many features are disabled in the free version
Free version lacks features like auto-save, PDF export, Markdown tables among many others and can't be used commercially.
Con Abandoned project
Nothing from author since 03/15. Pro version preview pane crashes, no fix has been offered. See user forums.
Con Preview window crashes / does not update
Con Not Free
Smartdown costs $19.99.
