There is a recent post on the Microsoft SQL Server Support Blog about how to get SQL Server 2008 and 2008 R2 installed on Windows Server 2008 R2. The issue is how you get the .NET Framework 3.5 SP1 installed (which is a prerequisite for both SQL Server 2008 and 2008 R2) onto Windows Server 2008 R2.
With Windows Server 2008, you could either install .NET 3.5 SP1 yourself before you started the SQL Server 2008/2008 R2 installation, or you could let the SQL Server 2008/2008 R2 installer take care of it. I usually chose the former, just to make the SQL Server installation go smoother and quicker.
Now, with Windows Server 2008 R2, you need to add the .NET 3.5 SP1 Framework as a Feature inside of Windows Server 2008 R2 by going onto Server Manager. The Microsoft blog post goes into step by step detail on how to do this. This may cause some issues at some shops where the DBA is not allowed direct access to the server, so you should be aware of this. I know that this caused me a few minutes of delay the first time that I ran into it a few months ago, as I was installing SQL Server 2008 on Windows Server 2008 R2 for the first time.
We are running all of our Production database servers on x64 SQL Server 2008 SP1 CU5 on Windows Server 2008 R2, with very good results since mid-November 2009. Microsoft made a lot of low level performance improvements in the scheduler in Windows Server 2008 R2, that are designed to allow SQL Server 2008 R2 to scale beyond 64 logical processors on x64. Even though I am “only” on SQL Server 2008 SP1, with 16 logical processors, I think some of these improvements in Windows Server 2008 R2 are beneficial even on smaller boxes like mine.