Below is a draft of a paper that I have been working on that explains how a multisignature cryptocurrency to cryptocurrency exchange should be designed. Multisignature has been around for a while but has yet to be used in an exchange. I believe it is an idea worth exploring in light of the near constant bad news we hear from various exchanges that gets broken into by attackers. The paper covers how such a exchange should be designed, and goes over some of the advantages and disadvantages of the design over a traditional exchange that uses a single exchange controlled private key to handle cryptocurrencies.
Multisig CryptoCurrency to CryptoCurrency Exchange , Draft 2/24/2015