I’d like to start a thread of a build check list for SharePoint 2013. From Infrastructure to Configuration of SharePoint services.
My suggestion is to generate a status of your brand new shiny farm’s infrastructure and SharePoint configuration using PowerShell script of your own, e.g. serialize all the objects you’re interested in (SharePoint, OS, etc.) into an XML file (or a bunch of XML files) on all the farm servers. And from time to time or during a troubleshooting session one can just check the difference between serialized target state of the farm and its current serialized state.