Master Page with Multiple Applications

I've been trying to find information on this but everything seems to be outdated (2005) and especially uses older versions of VS. I'm using Visual Studio 2012 or 2013 and I'm trying to use one master page and have multiple applications that call that master page. Reason is, I need to have separate application pools for each application. Right now, I have one for the whole site and just the main site as the application but if the application pool goes down, the whole site does. We have an older version running before we put out the new one and the older one has master pages in each folder (application) and so when an application pool messes up, one that section of the site is down. Is there a straight forward way to have one master for multiple web apps??