Update one instance of Sql Server 2008 R2 Standard to SP2? We have one server with multiple SQL Server 2008 R2 instances installed.  To support an application we need to upgrade one instance to SP2.  Can we only apply the service pack to the specific instance on the server, or would it have to be applied to all of the instances on the server?
Yes, you can choose which instance(s) you wish to apply the service pack. They'll all be checked by default; as will the client tools / shared features (there is only one "instance" of those):


  


You can re-run the installer later to update any that you didn't update this time; the ones that are already at SP2 will not be selectable.

On this VM, I have 2008 R2 RTM (no patches whatsoever) and 2008 R2 with Service Pack 2 and CU9, installed and running side by side with no issues:


  


Now, why you want to have a mix of patched and unpatched instances on a single server might be a different question...