I was surprised to discover that it's very easy to install the VMware Tools on Windows Server 2008 R2 Core today. Simply select the VM in VMware Infrastructure Web Access (assuming you are using VMware Server 2, if not use the appropriate interface) and click the Install VMware Tools link. The iso won't autorun, but all you have to do is change to the virtual CD–ROM drive within the VM (probably D:) and run:
msiexec /i "VMware Tools64.msi"

VMware Tools Installed
but only if you have ServerCore-WOW64 enabled/installed – as the installation is 32-bit even for the x64 2008 R2 OS
Hi gojj
Thanks for the comment and pointing this out – I probably already had ServerCore-WOW64 enabled/installed for other purposes.
Mike
OK, I am very late updating this, but after doing a fresh install today of Server 2008 R2 Core it seems that (in my environment at least) ServerCore-WOW64 was installed during Windows setup.