Q: Can I have a mix of application and desktop publishing in a single Remote Desktop Services collection on Windows Server 2012 R2?

A: No. By design, a collection can:

  • Publish desktops (session virtualization)
  • Publish applications
  • Serve virtual desktops (VDI)

If you need a mix, then you'll need separate collections (which are groups of Remote Desktop Session Hosts or Hyper-V servers for VDI) for each type of service. However, a single connection broker and web portal can be used to publish the services, which gives the end user a single interface to access all the different services.