I have inserted Markdown snippets in a Shiny app to write the documentation of the app easily (there is a tab "Documentation" where the user can learn how to use the app).
I also used Markdown in a Shiny app to generate automatic reports. Use the Shiny app to dive into the data. Once you have what's of interest to you, click "Export", the button calls the render function, pass a few arguments to an RMarkdown file, and automatically generate a report. The user can then share the report with his coworkers.