I think of drug companies and software companies as the two extreme examples. Drug development is basically a money-losing proposition without patents, because it takes millions to get to anything useful, and once you do it's distilled down into something that's almost trivially easy to copy.
With software on the other hand, innovation happens in tiny steps. Often patents are granted to ideas that took someone a few days to come up with. As software is built, hundreds or thousands of these ideas come together to (hopefully) create a high value application. Once you have a high value application as long as you don't release the source code it's not easy to copy. The patents don't help someone recreate it. They have to pour blood and sweat into the codebase to come up with something that actually replicates the value. In other words the patent helps no one but the trolls.
Of course this is obvious to any software developer which is why we reflexively assume patents are bad. However in between software and drugs, in the space real physical inventions, things are quite a bit grayer. In the case of physical things, the "obviousness" test is a little easier to apply because everyone has some familiarity with tools and objects, and R&D can be fairly expensive for a lot of simple end products. It seems to me that the underlying theory of patents is fundamentally sound, but just has absolutely no applicability to software.