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.