Citrix has released a whitepaper titled:"Windows 2008 R2 Optimization Guide For Desktop Virtualization with XenApp 6 / 6.5", the paper which contains 23 pages outlines optimization for XenApp 6 and 6.5 on Windows Server 2008 R2.
The paper starts with recommended GPO’s which can be applied to Windows Server 2008 R2, secondly it provides some recommendations on to be modified registry keys, which preferably can be set using Group Policy Preferences (GPP). It will then provide some registry keys to modify for images deployed using standard disk mode vDisk images using Citrix Provisioning Services.
After that the document recommends to disable some of the Services available on Windows Server 2008 R2, as they significantly increase the memory footprint of the OS. It also provides some recommendations on tuning SMB on Windows File Servers.
The second part focuses on general settings for users, preferably set using GPO or GPP. And then focuses on XenApp specific settings for users.