if ever you find yourself wondering why your vagrant box has suddenly stopped loading your website, and you have the passenger gem installed, there's a big possibility that it has automatically upgraded the gem and needs you to make a few changes to the apache module for it. This is just one issue I have come across.
So in light of sharing the knowledge just open the following file for editing on the command using your preferred editor if you're running apache.
/etc/apache2/conf.d/passenger
and replace the three lines with the following:
. LoadModule passenger_module /var/lib/gems/1.9.1/gems/passenger-4.0.10/buildout/apache2/mod_passenger.so
PassengerRoot /var/lib/gems/1.9.1/gems/passenger-4.0.10
PassengerDefaultRuby /usr/bin/ruby1.9.1
we're basically replacing the version number the module should use.