A brief post based on experience.
Recommended: In-place upgrade of vCenter
The in-place upgrade from vCenter 4.1 to vCenter 5 is a quick and easy process. With the upgrade there would be less than one hours downtime whilst desktop groups should be in maintenance mode and the Citrix XenDesktop Controller will not be able to control the power state of virtual desktops, but end users can still continue to work (if a user is already logged on, maintenance mode takes effect as soon as they log off.)
A vCenter rebuild would have incurred having to add the new vCenter as a host in Citrix Desktop Studio, and further re-add all desktops, and re-create any catalogs.
Recommended: In-place upgrade of ESXi hosts
The in-place upgrade from ESXi 4.1 to 5 is a quick and easy process via vCenter 5 Update Manager, and saves having to reconfigure hosts and remount any NFS datastores (NFS is recommended for VDI deployments due to its scalability,) especially in environments where Host Profiles and/or Auto Deploy is not an option due to host licensing (i.e. not Enterprise Plus.)
The Citrix XenDesktop Controller communicates with the vCenter Server, and the recommendation regarding upgrading the ESXi hosts is just here for completeness.
Warning: When installing/upgrading VMware Tools to vSphere 5
Use the Custom Installation option to deselect the SVGA 3D Driver under the VMware Device Drivers feature set.
See the following articles for more information:
http://support.citrix.com/article/CTX124877 - Unable to Connect to XenDesktop Virtual Desktop Agent on Vista or Windows 7 with WDDM Driver
http://support.citrix.com/article/CTX123952 - Unable to Connect to XenDesktop Virtual Desktop Agent on Windows 7 with VMware Tools ESX 4.0 Update 1
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