In light of the MF Global/CME situation, Jim Sinclair put out an email bulletin last night (see link below) recommending all stock owners to request their certificates or use the "direct registration" method for securing their ownership. Awhile back I think I remember Sinclair saying that if more owners would use these 2 methods to secure stock ownership, this would definitely reduce the shorting on these companies where sufficient numbers of shareholders were willing to take a stand against the unauthorized borrowing of their shares. I'm not sure it would stop naked shorting.
http://www.jsmineset.com/2011/12/03/direct-registration-faq/