Hi all,
This is a great question and one we aimed to tackle in Shiny Server Pro. ShinyApps will also expose the ability to ask users to login before granting them access to the app. You can use things like LDAP and Active Directory if you're deploying inside an organization, but you may be more interested in the soon-to-be-released Google auth feature. This feature will allow users to login using their Google account which is exposed to your Shiny application.
This allows you to store settings or data unique to the current user in a Shiny process. We'll be working to put together more examples of this functionality over the coming weeks and will certainly have something ready by the time we launch the feature on ShinyApps.io.
FYI Andrew, ShinyApps will eventually be replacing Glimmer and Spark. We're not in a rush, but the stability, scalability, and reliability of ShinyApps will be much greater. We'll also be rolling out new features like authentication uniquely on ShinyApps moving forward. So take it for a spin when you have a chance and let us know what you think!
Best,
Jeff