When new products are released, it generally takes a few weeks before Microsoft's other products get full support. This time, when Windows 8.1 andR2 was released, we saw a bit different story. In October 2013, Microsoft hit us with a tidal wave of product updates and in this tidal wave they made sure that System Center 2012 R2 completely supported the latest operating system updates out of the gate. This is truly a welcome change.
However, the older System Center products still under support did not receive the same supportability for Windows 8.1 and Windows Server 2012 R2. That continues to follow the old path, but Microsoft has now issued a statement that ConfigMgr 2012 SP1, ConfigMgr 2007 SP2, Endpoint Protection SP1, and Forefront Endpoint Protection 2010 have all received the stamp of support approval – after applying some necessary updates.
System Center 2012 Configuration Manager SP1 supports Windows Server 2012 R2 and Windows 8.1 with the following update: Cumulative Update 3 for System Center 2012 Configuration Manager SP1 – KB 2882125
System Center Configuration Manager 2007 SP2 supports Windows Server 2012 R2 and Windows 8.1 as Configuration Manager Clients with this update: An update is available that adds support for Windows 8.1 and Windows Server 2012 R2 to System Center Configuration Manager 2007 Service Pack 2
System Center 2012 Endpoint Protection SP1 and Forefront Endpoint Protection (FEP) 2010 (with Update Rollup1) supports Windows Server 2012 R2 and Windows 8.1 if you apply this update: An anti-malware platform update for Endpoint Protection clients is available from Microsoft Support
There's some additional caveats, too, like which OS's can host a distribution point and whether or not ConfigMgr 2007 will support OS deployment for these new operating systems, so you'll want to read through the full statement: