Overall, though, the transition should be more of an annoyance than anything else, Pironti says. As certificates issued to businesses expire, they are generally replaced with certs using longer keys, he says, so there might not be so many that remain in use.

There are commercial tools for finding and automatically replacing certificates that are too short, Pironti says. Among them is Director made by Venafi, which contributed to the latest NIST Information Technology Laboratory on certificate authority compromise and fraudulent certificates.

NIST currently has set a deadline of Dec. 31, 2013 for when entities ought to stop using 1024-bit RSA and DSA encryption. "However, since such keys are more and more likely to be broken as the 2013 date approaches, the data owner must understand and accept the risk of continuing to use these keys to generate digital signatures," according to a special publication called "" published in 2011.

Microsoft is updating its operating systems in the wake of the Flame malware used to spy on networks in Iran. Flame exploited Micrsoft's use of the MD5 hashing algorithm in authenticating Windows Update. Microsoft officially disallowed its use in 2009 but failed to weed it out of its own products, particularly Terminal Server Licensing Service. Researchers figured out how to compromise MD5 using what they call collision attacks to obtain fraudulent certificates that are accepted as real.

Since Flame was publicized, Microsoft has started a campaign not only to shut down use of MD5 but also beef up other areas that have not fallen victim to attackers.