I usually steer clear of controversial subjects such as the notion of software patents, mainly because I am somewhat conflicted on the subject myself since I've filed for patents here at Borland. On one hand, one should be able to gain patent protection for a new and unique invention (or in the case of software, a process). On the other hand, with the seemingly whacky patents that have been granted over the years for what many agree are obvious uses of existing technology (can you say, OneClick?). Well it seems that the U.S. Supreme Court is actually going to hear a case and possibly rule on what should be considered "obvious to a person of ordinary skill in the art." This article on ArsTechnica outlines this case. There's also some links to the actual petition. What is really interesting in this case is that the petioner actually won their case in the U.S. Court of Appeals! However they felt that the court didn't rule on the premise of their argument which is based on a 1952 federal law regarding the obviousness of an idea or invention.
Regardless of what side one falls on the whole notion of whether or not software should be patented, the fact of the matter is that software is patented. So if you refuse to file for patent protection on your new and unique ideas simply on principle, you may find that that is all you've got to fall back on when someone becomes wildly successful based on your idea. Or even worse, comes after you with an infringement suit because they patented the idea. Until the current U.S. patent system is reformed or at least clarified, your only choice is to take a defensive stance and try and patent as much as you can. In many cases the best you can hope for is a stalement if someone comes after you with an infringement suit. If you have your own portfolio of patents, chances are the person filing suit against you may be infringing on one of yours. So the only recourse you have is to cross-license the patents. If you had nothing in your portfolio, then you could be liable for major damages including on-going license fees. The really nasty kicker is that if the plaintiff can show that you had prior knowledge of a particular patent and infringed anyway, you could be liable for triple damages!
Whether or not this case presented to the U.S. Supreme Court has any affect on the patent system remains to be seen. It does, however, look to be a step in the right direction.