diff --git a/.yardopts b/.yardopts
new file mode 100644
index 00000000..a4541bea
--- /dev/null
+++ b/.yardopts
@@ -0,0 +1 @@
+-m markdown
diff --git a/Gemfile b/Gemfile
index 4da9e50b..a2fbe46a 100644
--- a/Gemfile
+++ b/Gemfile
@@ -12,7 +12,10 @@ group :test do
   gem "rake"
   gem "contest", ">= 0.1.2"
   gem "mocha"
-  gem "yard"
+
+  # For documentation
+  gem "yard", "~> 0.6.1"
+  gem "bluecloth"
 
   platforms :mri_18 do
     gem "ruby-debug"
diff --git a/Gemfile.lock b/Gemfile.lock
index 8dd69ba2..41a32beb 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -24,6 +24,7 @@ GEM
   specs:
     abstract (1.0.0)
     archive-tar-minitar (0.5.2)
+    bluecloth (2.0.7)
     columnize (0.3.1)
     contest (0.1.2)
     erubis (2.6.6)
@@ -64,6 +65,7 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
+  bluecloth
   contest (>= 0.1.2)
   mocha
   rake
@@ -71,4 +73,4 @@ DEPENDENCIES
   ruby-debug19
   vagrant!
   virtualbox!
-  yard
+  yard (~> 0.6.1)
diff --git a/lib/vagrant/box.rb b/lib/vagrant/box.rb
index 437e05fc..af5d7591 100644
--- a/lib/vagrant/box.rb
+++ b/lib/vagrant/box.rb
@@ -4,7 +4,7 @@ module Vagrant
   # virtual machine, at the least. They are created with `vagrant package`
   # and may contain additional files if specified by the creator. This
   # class serves to help manage these boxes, although most of the logic
-  # is kicked out to actions.
+  # is kicked out to middlewares.
   class Box
     # The name of the box.
     attr_accessor :name
@@ -46,6 +46,8 @@ module Vagrant
     # virtual machine file which contains specifications of the exported
     # virtual machine this box contains.
     #
+    # This will only be valid once the box is imported.
+    #
     # @return [String]
     def ovf_file
       directory.join(env.config.vm.box_ovf)
@@ -53,12 +55,12 @@ module Vagrant
 
     # Begins the process of adding a box to the vagrant installation. This
     # method requires that `name` and `uri` be set. The logic of this method
-    # is kicked out to the {Actions::Box::Add add box} action.
+    # is kicked out to the `box_add` registered middleware.
     def add
       env.actions.run(:box_add, { "box" => self })
     end
 
-    # Begins the process of destroying this box.
+    # Begins the process of destroying this box. This cannot be undone!
     def destroy
       env.actions.run(:box_remove, { "box" => self })
     end
@@ -69,14 +71,16 @@ module Vagrant
     end
 
     # Returns the directory to the location of this boxes content in the local
-    # filesystem.
+    # filesystem. Note that if the box isn't imported yet, then the path may not
+    # yet exist, but still represents where the box will be imported to.
     #
     # @return [String]
     def directory
       env.boxes_path.join(name)
     end
 
-    # Implemented for comparison with other boxes.
+    # Implemented for comparison with other boxes. Comparison is implemented
+    # by simply comparing name.
     def <=>(other)
       return super if !other.is_a?(self.class)
       name <=> other.name
diff --git a/lib/vagrant/cli.rb b/lib/vagrant/cli.rb
index db0f4fec..40decec4 100644
--- a/lib/vagrant/cli.rb
+++ b/lib/vagrant/cli.rb
@@ -4,9 +4,32 @@ module Vagrant
   # Entrypoint for the Vagrant CLI. This class should never be
   # initialized directly (like a typical Thor class). Instead,
   # use {Environment#cli} to invoke the CLI.
+  #
+  # # Defining Custom CLI Commands
+  #
+  # If you're looking to define custom CLI commands, then look at
+  # one of the two following classes:
+  #
+  # * {Command::Base} - Implementing a single command such as `vagrant up`, e.g.
+  #   one without subcommands. Also take a look at {Command::NamedBase}.
+  # * {Command::GroupBase} - Implementing a command with subcommands, such as
+  #   `vagrant box`, which has the `list`, `add`, etc. subcommands.
+  #
+  # The above linked classes contain the main documentation for each
+  # type of command.
   class CLI < Thor
     # Registers the given class with the CLI so it can be accessed.
-    # The class must be a subclass of either {Command} or {GroupCommand}.
+    # The class must be a subclass of either {Command::Base} or {Command::GroupBase}.
+    # Don't call this method directly, instead call the {Command::Base.register}
+    # or {Command::GroupBase.register} methods.
+    #
+    # @param [Class] klass Command class
+    # @param [String] name Command name, accessed at `vagrant NAME`
+    # @param [String] usage Command usage, such as "vagrant NAME [--option]"
+    # @param [String] description Description of the command shown during the
+    #   command listing.
+    # @param [Hash] opts Other options (not gone into detail here, look at
+    #   the source instead).
     def self.register(klass, name, usage, description, opts=nil)
       opts ||= {}
 
diff --git a/lib/vagrant/command/base.rb b/lib/vagrant/command/base.rb
index 9ccf4c3d..c2d8b440 100644
--- a/lib/vagrant/command/base.rb
+++ b/lib/vagrant/command/base.rb
@@ -3,7 +3,7 @@ require 'thor/actions'
 
 module Vagrant
   module Command
-    # A CLI command is the subclass for all commands which are single
+    # A {Base} is the superclass for all commands which are single
     # commands, e.g. `vagrant init`, `vagrant up`. Not commands like
     # `vagrant box add`. For commands which have more subcommands, use
     # a {GroupBase}.
@@ -15,7 +15,50 @@ module Vagrant
     # the command is invoked, it must be made `protected` or `private`.
     #
     # The best way to get examples of how to create your own command is to
-    # view the various Vagrant commands, which are relatively simple.
+    # view the various Vagrant commands, which are relatively simple, and
+    # can be found in the Vagrant source tree at `lib/vagrant/command/`.
+    #
+    # # Defining a New Command
+    #
+    # To define a new single command, create a new class which inherits
+    # from this class, then call {register} to register the command. That's
+    # it! When the command is invoked, _all public methods_ will be called.
+    # Below is an example `SayHello` class:
+    #
+    #     class SayHello < Vagrant::Command::Base
+    #       register "hello", "Says hello"
+    #
+    #       def hello
+    #         env.ui.info "Hello"
+    #       end
+    #     end
+    #
+    # In this case, the above class is invokable via `vagrant hello`. To give
+    # this a try, just copy and paste the above into a Vagrantfile somewhere.
+    # The command will be available for that project!
+    #
+    # Also note that the above example uses `env.ui` to output. It is recommended
+    # you use this instead of raw "puts" since it is configurable and provides
+    # additional functionality, such as colors and asking for user input. See
+    # the {UI} class for more information.
+    #
+    # ## Defining Command-line Options
+    #
+    # Most command line actions won't be as simple as `vagrant hello`, and will
+    # probably require parameters or switches. Luckily, Thor makes adding these
+    # easy:
+    #
+    #     class SayHello < Vagrant::Command::Base
+    #       register "hello", "Says hello"
+    #       argument :name, :type => :string
+    #
+    #       def hello
+    #         env.ui.info "Hello, #{name}"
+    #       end
+    #     end
+    #
+    # Then, the above can be invoked with `vagrant hello Mitchell` which would
+    # output "Hello, Mitchell"
     class Base < Thor::Group
       include Thor::Actions
       include Helpers
diff --git a/lib/vagrant/config.rb b/lib/vagrant/config.rb
index 54b76766..a59402c1 100644
--- a/lib/vagrant/config.rb
+++ b/lib/vagrant/config.rb
@@ -2,8 +2,27 @@ require 'vagrant/config/base'
 require 'vagrant/config/error_recorder'
 
 module Vagrant
-  # The config class is responsible for loading Vagrant configurations
-  # (usually through Vagrantfiles).
+  # The config class is responsible for loading Vagrant configurations, which
+  # are usually found in Vagrantfiles but may also be procs. The loading is done
+  # by specifying a queue of files or procs that are for configuration, and then
+  # executing them. The config loader will run each item in the queue, so that
+  # configuration from later items overwrite that from earlier items. This is how
+  # Vagrant "scoping" of Vagranfiles is implemented.
+  #
+  # If you're looking to create your own configuration classes, see {Base}.
+  #
+  # # Loading Configuration Files
+  #
+  # If you are in fact looking to load configuration files, then this is the
+  # class you are looking for. Loading configuration is quite easy. The following
+  # example assumes `env` is already a loaded instance of {Environment}:
+  #
+  #     config = Vagrant::Config.new(env)
+  #     config.queue << "/path/to/some/Vagrantfile"
+  #     result = config.load!
+  #
+  #     p "Your box is: #{result.vm.box}"
+  #
   class Config
     extend Util::StackedProcRunner
 
@@ -12,6 +31,12 @@ module Vagrant
     attr_reader :queue
 
     class << self
+      # Resets the current loaded config object to the specified environment.
+      # This clears the proc stack and initializes a new {Top} for loading.
+      # This method shouldn't be called directly, instead use an instance of this
+      # class for config loading.
+      #
+      # @param [Environment] env
       def reset!(env=nil)
         @@config = nil
         proc_stack.clear
@@ -20,14 +45,29 @@ module Vagrant
         config(env)
       end
 
+      # Returns the current {Top} configuration object. While this is still
+      # here for implementation purposes, it shouldn't be called directly. Instead,
+      # use an instance of this class.
       def config(env=nil)
         @@config ||= Config::Top.new(env)
       end
 
+      # Adds the given proc/block to the stack of config procs which are all
+      # run later on a single config object. This is the main way to configure
+      # Vagrant, and is how all Vagrantfiles are formatted:
+      #
+      #     Vagrant::Config.run do |config|
+      #       # ...
+      #     end
+      #
       def run(&block)
         push_proc(&block)
       end
 
+      # Executes all the config procs onto the currently loaded {Top} object,
+      # and returns the final configured object. This also validates the
+      # configuration by calling {Top#validate!} on every configuration
+      # class.
       def execute!(config_object=nil)
         config_object ||= config
 
@@ -37,6 +77,10 @@ module Vagrant
       end
     end
 
+    # Initialize a {Config} object for the given {Environment}.
+    #
+    # @param [Environment] env Environment which config object will be part
+    #   of.
     def initialize(env)
       @env = env
       @queue = []
@@ -65,14 +109,24 @@ module Vagrant
   end
 
   class Config
+    # This class is the "top" configure class, which handles registering
+    # other configuration classes as well as validation of all configured
+    # classes. This is the object which is returned by {Environment#config}
+    # and has accessors to all other configuration classes.
+    #
+    # If you're looking to create your own configuration class, see {Base}.
     class Top < Base
       @@configures = []
 
       class << self
+        # The list of registered configuration classes as well as the key
+        # they're registered under.
         def configures_list
           @@configures ||= []
         end
 
+        # Registers a configuration class with the given key. This method shouldn't
+        # be called. Instead, inherit from {Base} and call {Base.configures}.
         def configures(key, klass)
           configures_list << [key, klass]
           attr_reader key.to_sym
@@ -90,7 +144,10 @@ module Vagrant
       end
 
       # Validates the configuration classes of this instance and raises an
-      # exception if they are invalid.
+      # exception if they are invalid. If you are implementing a custom configuration
+      # class, the method you want to implement is {Base#validate}. This is
+      # the method that checks all the validation, not one which defines
+      # validation rules.
       def validate!
         # Validate each of the configured classes and store the results into
         # a hash.