Three things:

First off a fairly MST style badfic rant by my friend Dan-chan, which I'm sure you will all enjoy. Because I have rarely read badfic worse than she found. Non-fandom.

http://community.livejournal.com/badrperssuck/7426965.html

Secondly, a link to an Uber Sue fic written by another friend Pip. It's set in Bleach, suffers from a sugar overdose but does accurately portray how painfully Sues can warp canon-reality.

http://www.fanfiction.net/s/4667732/1/SparkleMarysue

And an extract:
Yoruichi would never call out her sword, never allow herself to use her supposed 'partner' no matter how dire the situation. Wincing she sealed the oath with the binding words, "Mary…sue…"

--

'Actually' an angelic voice whispered, so angelic that as she spoke the sun brightened and she received her own styling of font, 'my name is Maria Amaya Nefretiri Phoenix Susanna Fire de Pompadour the 4th' Yoruichi's eye twitched…again. 'not 'Mary-Sue'

"See…I would say that but I'd be killed just trying to perform Shikai…"

And in a nutshell: 'Of course!' Chirped the irritatingly perfect voice; 'It is one of my 4,000,000,000 rare powers!'


Finally, although I don't have the attention span to join missions myself, I thought it might be quite amusing to have an agent who was a captured, semi-tamed Mary Sue that could be pitched against severe cases. A muzzle and a power-dampening chain should do the trick. ^^

I'm afraid I don't know whether this has been done already.