In case you haven't seen these links, there are two new papers published on how Microsoft deployed ConfigMgr in our desktop environment. Quite a few of the blog posts on this System Center in Action page are related to the work that went into the deployment over a two year time period. 

 The first paper linked below is the main paper on all up deployment: http://technet.microsoft.com/en-us/library/hh913620.aspx

 

The second paper is specifically related to implementing the Application Catalog:  http://technet.microsoft.com/en-us/library/hh925141.aspx

 

There's a third paper in the works on security & management in System Center 2012 Configuration Manager.  More to come on this final paper.