But patenting covers independent inventions of the same algorithms. And it's frequently used for ideas that are profoundly obvious, like a straightforward application of machine learning techniques to a particular data set (Bilski). So if you think of an idea by yourself, you can be sued for implementing it.
As a developer, it is recommended that I not read patents, as if it is determined that I read a patent that I then violated, it will be triple damages in a lawsuit. So I have no way to avoid implementing somebody else's patent.
Now Sony's lawsuit isn't about software, or patents. It is about certain special secret integers. It so happens that used with readily available software they blow a wide hole in Sony's horrible security system for the PS3.
But Sony doesn't own those integers. It doesn't own the hardware it sold to people under pretenses that it would always run Linux, and it doesn't have the right to control how people would choose to use their hardware and GPU. Hotz never used PSN software or any of Sony's other products.