What is Rakudo? Rakudo is the implementation of the Perl 6 spec on the Parrot virtual machine. I call Rakudo a "flavor" because any implementation of Perl 6 that passes the Perl 6 test suite can call itself Perl 6. Perl 5 spec and implementation were one and the same, which meant that any additional implementation that could have ever hoped to be written (which never happened) would have had to be bug-for-bug compatible with the original implementation of Perl 5, because that was the spec. Perl 6 does not repeat this mistake and actually is currently benefiting already from the principle. Pugs was an initial prototype of Perl 6 with the Haskell programming language, which is no longer actively maintained, but it's extensive test suite is currently being converted into the Perl 6 test suite. The pugs test directory is actually an svn external and lives at languages/perl6/t/spec in the Parrot svn repository. As you can see, Rakudo and the Perl 6 test suite still live inside the Parrot repository. This will probably change sometime next year as Parrot gets closer to 1.0 and Rakudo can be built on a fully functional Parrot.
This isn't supposed to make a lot of sense, but you can metaphorically think of Rakudo as the Fourier Transform of Perl5: