I bought a new pair of wireless headphones a few months ago. I'd always heard that wireless audio was a really dumb idea because of the sound quality, but I really wanted to get rid of that cable.
After some research, I discovered that there's a particular Bluetooth audio codec called apt-X, which has essentially wired sound quality (and certainly way better than the awful default Bluetooth audio). No cables, no dongles (my mac supports apt-X out of the box).
This represents a genuine (patented) innovation - none of the other wireless audio solutions are as good. I can't help but wonder if the people behind it would have bothered if they couldn't patent the codec.
I don't know if that makes the patent system worth it for software. I suspect it doesn't. But I know at least one example where it led to innovation that may not have happened otherwise.