If you ever find yourself in the situation that you want to be able to only publish applications or desktops to your users you can can create two stores (1 for the applications and the other for desktops). You can configure both stores to point to the same XenApp/XenDesktop farm/site. This blog post by Feng Huang describes the configuration of the StoreFront Store in great detail. When you have this configured and you connect to the Desktops only store, you are only able to (re)connect to desktops. Any opened or disconnected published applications won’t be reconnected from that store. Vice versa this works off course the same, open or disconnected published desktop(s) aren’t reconnected when connecting to the Applications only store.