My colleague spent some time in the TrustLab today installing VMware vCenter Protect Update Catalog. This was previously a solution from Shavlik and provides update management of third party applications such as Adobe Reader, QuickTime, Sun Java etc directly from within System Center 2007/2012 Configuration Manager alongside the normal Microsoft patch updates.
You can find Part 1 of his blog post on the installation here: http://ixrv.blogspot.co.uk/2012/06/configuring-scup-2011-shavlikvmware.html
More info on vCenter Protect Update Catalog (They need a better name!) can be found here: