There is a new file format called msu or Microsoft Update Standalone package. These are hotfixes meant for Vista and new OS. It is also used for the installation of Vista OS, but I have not tried digging to that detail.
The msu file is a compressed file archive of a cab file, xml and a text file. The xml file is the installer config file. If you are handling at the msu file level, use the Windows Update Stand-alone Installer or Wusa.exe. If you are going to use SMS or SCCM to push it out, you will need to play with expanded file and the package manager, pkgmgr.exe. The pkgmgr is the actual program that does the heavy lifting with xml file.