Both Commerce Server 2007 and Commerce Server 2009 have been tested on Windows Server 2008 R2 and both are fully supported on this platform. However there are a few items that I wanted to review regarding either upgrading or installing either version of Commerce Server on this platform.
For Commerce Server 2007, there are no issues with performing a new installation on Window Server 2008 R2. However, once the installation is complete and the configuration wizard has finished setting up the initial server databases you will need to install Commerce Server 2007 Service Pack 2 to be in a supported state. You will want to complete the service pack installation before you setup any Commerce sites on the server. If you are performing an operating system upgrade to an existing Commerce Server 2007 deployment, you should install Commerce Server 2007 Service Pack 2 and run the upgrade wizard against each Commerce site already deployed and verify that all site functionality prior to the operating system upgrade.
For Commerce Server 2009, there is an additional step that will need to be performed prior to the installation. With the installation of Commerce Server 2009 CD2 it performs a check for .NET Framework 3.5 SP1 and does this check by looking for a registry key stating that it has been installed. With Windows Server 2008 R2 the framework is already built-in to the operating system and therefore the registry key showing that it has been installed is not present. There is an update that you will need to obtain to resolve the installation issue which can be found in Microsoft Knowledge Base Article 975567; http://support.microsoft.com/default.aspx?scid=kb;EN-US;975567. You will want to obtain the update and run it against your server prior to the installation of either CD1 or CD2 of Commerce Server 2009. When you run the update it will perform a single check for the registry key and if present let you know that the update is not needed and do nothing, but if it is not present then it will add the registry entry and then exit. After the update is applied you can perform the installation of Commerce Server 2009 normally. If you are performing an operating system upgrade to a server that is already running Commerce Server 2009 there is no need to obtain the update as Commerce Server 2009 is already installed and the required components are already in place.