Patents make sense when seeing an idea through to its fruition requires requires a significant risk. New drugs and new hardware often have such requirements. The protection therefore must be equative to the risk. Most software ideas that are patented do not meet this criterion.
Software CEOs with shareholders but who also don't happen to agree with the idea of patenting software (like myself) are put in an awkward position. Because software patents exist, they make a company more valuable and are required in some situations to protect the company. At Real Software, we have applied for patents on technology developed for Real Studio even though we disagree that they should exist because we have a fiduciary responsibility to our shareholders and want to protect our customers as well. Software patents are an evil we must deal with as long as they continue to exist.
It is my hope that the President, Congress and future leaders will continue to examine and refine the patent process to protect those that deserve protection and stop protecting those that use it to stifle innovation or extort money from smaller companies who can't afford to defend themselves even when they are in the right. I encourage those of you in the US to contact your representatives in Congress and ask them take part in this important discussion.