If you know or have a strong reason to believe that you are about to violate someone's patent, stop, think, think again, think some more, and keep on thinking until you lose interest in doing something that might bankrupt you. Right and wrong are nice principles to live by, but they don't really mean much in court.

Every piece of nontrivial code infringes on somebody's patent. When people are patenting double clicking and doubly-linked lists, you can't help but infringe on somebody's patent. Stopping development while the lawyers work out a deal every time you hit a patent would destroy programmer productivity.

A good chunk of these patents would be quickly thrown out if they ever went to court. It's in the best interests of the litigant to make sure things never get there. They offer a reasonable settlement and then go find another company to harass.

The only defense companies have against this is to accumulate a pile of their own patents. If a company sues them, the litigant almost certainly is infringing on their patents, so they can counter-sue. Then everything gets dropped. This game favors big companies--small ones wouldn't be able to accumulate enough patents to defend themselves.

So you're correct, trying to stand up for your ideals is impractical in court, but giving in is an equally bad strategy. Patent law and the surrounding bureaucracy is simply unequipped to handle software right now.

I don't think software patents are necessarily bad, and there are some algorithms that deserve a patent. But the system is completely out of hand as it is.