Most - if not all - software patents are bogus.
Many years ago I saw a lawyer say that he had examined a random sample of IBM's software patents, and estimated that about 70% of them wouldn't stand up in court. And it was his belief that IBM had better patents than most companies out there. The problem was, of course, that if they drop a stack of 15 patents on you neither you nor they know what they will get to stick, but they will definitely get you with something.
And why not file those patents? Their main purpose is to be an unused threat, and they are threatening whether or not they are used.
Therefore even by the very relaxed standards the that US legal system does, most software patents are bogus. If you hold a higher intellectual standard, then it isn't hard for that 70% to become 100%, or close enough to it to make the exceptions negligible.
(There is hope that Bilski will restore some sanity to the US system.)