I did a migration last week at a clients site from Windows 2003 Presentation Server 4.5, Provisioning Server 4.5 and Web Interface 4.6 to Windows 2008 XenApp 5, Provisioning Server 5.1a and Web Interface 5.
During the image build for Windows 2008 XenApp I had a few issue that were resolved by installing these 5 Windows 2008 hot fixes from Microsoft.
- http://support.microsoft.com/kb/951149/en-us – “Stop error on a Windows Server 2008-based terminal server when the server is running under a heavy load: 0x0000000A”
- http://support.microsoft.com/kb/949914 – “Citrix ICA clients may crash when they are connecting to a Windows Server 2008-based terminal server that has Citrix Presentation Server installed”
- http://support.microsoft.com/kb/955625 – “Mandatory user profiles do not work as expected on Windows Vista-based and Windows Server 2008-based client computers when the %LogonServer% environment variable is set in the profile path”
- http://support.microsoft.com/kb/953531 – “A 0x0000007E Stop error occurs in Windows Server 2008 after you unmount and delete a persistent VSS snapshot”
- http://support.microsoft.com/kb/958652 – “Some Citrix commands do not work correctly in Citrix XenApp 5.0 for Windows Server 2008”
Jeremy Waldrop's Blog 
It’s not a Microsoft hotfix but this one is pretty much a MUST have too: http://support.citrix.com/article/CTX119793
thank you, I saw that this hotfix was released last week. Before this hotfix I was having to use adsiedit to fix the SPN after adding new devices.