I'm planning of upgrading my physical server nodes to the latest service pack for Server 2008 R2.
In order to do this with as little downtime, I'm going to live migrate all VM's on one node to another so I can do the upgrade and then live migrate them back.
My question is whether the VM's will work on an upgraded service pack once they have been migrated over.
Live Migrating from one version of Windows to another (even just a service pack) is not a good idea™.
When upgrading a cluster you should shutdown the cluster services, upgrade, then start everything back up. In the case of Hyper-V VMs, you should do an actual shutdown (or turn off), not hibernate/save-state/etc.
SP1 is still in Beta, and I've experience a bit of strangeness in my test systems; I would highly recommend you wait for the RTM.
You might find you need to update the integration components in each guest (and might have a performance reduction until you do).
But, SP1 for Windows 2008 R2 is currently in beta test, expected to be released (alongside Windows 7 SP1) in the first half of next year. If you are concerned about uptime you should not be running test software unless you have no choice.
EDIT, 2010-10-26: MS has just released release candidates of Windows 7 SP1 and Server 2008 R2 today: http://blogs.technet.com/b/windowsserver/archive/2010/10/26/service-pack-1-release-candidate-now-available.aspx