Hrmm.. I myself am not writing one with Shredder, but I know of some folks who have.
True Forces by Sue Stitler, taken from the movie universe. It's long, but it's damn good (if not... "gut wrenching!")
And some fics by Andrew Modeen on Shredder himself...
*kicks Fortunecities for not coming up* Well.. unfortunatley I can't get those links cause I can't access the Fic Archive. But this is the Archive link.. just look for those two authors, and you'll get the links to the fics.
http://www.fortunecity.com/skyscraper/photoshop/1828