Shortly after I started reading fanfiction I found out what a Mary Sue was. Then I started reading Mary Sue Parodies, 'cause it is fun to poke at the cliches. Sadly, there is a lot of tripe out there. Writing a parody is by no means any easier than writing a regular story. In a parody too you need a plot before you start writing. Shear randomness is not fun. Randomness must have a function in the story. But there are some good, very funny Mary Sue parodies among the many that are written. Some of them are linked here (at least I hope this list isn't exhaustive).
I started a C2-archive on Fanfiction.net where I tried to collect the best FF.net had to offer when it came to Mary Sue Parodies. The title of the archive is a pun on the song Peggy Sue by Buddy Holly (as if you didn't know). The tagline I used was: when Mary Sue brings tears to our eyes, it should be tears of joy. I still feel that way, so here I bring you a selection from that archive: Oh, Mary Sue Archive
Protectors of the Plot Continuum is an organisation founded by Jay and
Acacia and started out in the fandom of Lord of the Rings. Protectors
are assassins, though some prefer the term agents, who go into a story
and take out the Sue -- after she has been properly charged with crimes
against the fandom and fanfiction in general.
I've tried my hand at a PPC spin off myself. These stories can be found
here
Others have also tried their hands on Protectors missions. The most
complete overview of these missions can be found on the
PPC wiki
MST is short for Mystery Science Theater 3000. In fanfiction it is the fine art of mocking every line of a truely bad fic. My MSTings.