If you’re looking for automation / unattended installation of Citrix XenApp 4.5 / 5 check here : XenApp 4.5 / 5 unattended installation
If you need to industrialize the installation of Citrix XenApp 6, you can follow this blog to create a new farm using command line and add a new XenApp server to an existing farm. On my side, I used the scripts you’ll read bellow with a deployment software (Altiris, SCCM etc…)
Unattended XenApp 6 farm creation
Before begging to install XenApp 6 you need to add one role and one feature to your Windows 2008 R2 server. To do so, you need to use PowerShell since servermanagercmd.exe reach his end of life.
Open a PowerShell shell and type Import-Module Servermanager to Load the Server Manager module into the Windows PowerShell session before working with Server Manager cmdlets. Once it’s done, you need to type this two command lines to add the .NET Framework 3.5.1 feature and the Remote Desktop Session Host role