Nice overview of most of these file types and more in this great overview blog entry.
Gemfile (Ruby) - is used to manage installation and dependencies for Ruby gems. It's read and processed by bundler.
Berksfile is used to manage installation and dependencies for cookbooks (much like Gemfile manages gems).
Guardfile is used to describe how to watch files and folders and execute commands automatically if they change. Often it's used to run some of the automated linting and testing commands like rubocop, foodcritic, chefspec/rspec.
Thorfile (Ruby) is a command line helper description file that provides documentation and hints on what command line parameters are expected by certain commands.
Rakefile (Ruby) is for organizing tasks to run (like the original old school Makefile) in Ruby code.
Vagrantfile contains instructions for the virtual machine manager, Vagrant, for automatically creating and provisioning VM's. Often Virtualbox is the most common VM hypervisor provider but many are available including VMWare, Hyper-V, and Parallels. In addition to Hypervisors plug-ins are available to provider Docker containers as well as various cloud providers (EC2, Azure, Google, Joyent, etc).
Dockerfile contains instructions for Docker to provision new containers.