I've wanted to write about this for ages...Finally we've announced System Center Mobile Device Manager (SCMDM) - it's due to be released in the first half of next year. Today the story for managing Windows Mobile devices centered around Exchange Server 2007 which provides the means to enforce basic policy and remote wipe lost or stolen devices.
SCMDM will take us much further. Windows Mobile 6 devices will become fully fledged domain members thereby coming in the remit of active directory group policy --> fine grained control. We will provide a state of the art mobile virtual private network connectivity feature and introduce 130 new group policy controls. The new product will provide the infrastructure for all manner of third party applications to be securely accessible via mobile devices.
Jason wrote a nice summary of SCMDM's features and presented a webcast (Live Meeting session) going into more detail - you can view the recording here