When Amazon patented A 1 click button. They were not talking about an algorithm, they were talking about the idea of having a button which purchases the object I want with 1 click. Implementation of this is wide, this patent tells me nothing of what the process behind the patent should be. If it did then you could get around it. That's the fundamental issue with those patents as you've pointed out. I can't figure out what is or isn't an implementation of this patent because no real useful implementation instruction was given.

On the other hand The Marching Cube algorithm patent does fit what you are talking about, the is instruction on how to implement the algorithm and those kind of patents have some issue for sure too. The claim against it was that it's a completely obvious way to solve the problem. There are alternatives to this algorithm such as the (http://en.wikipedia.org/wiki/Marching_Tetrahedrons) which is just redoing the same thing another way, so it's at least better to me than the 1 click patent.

Software patents in general are wrong, I'm not arguing against that but saying all software patents do is patent algorithms is not strong enough an attack in my view. When people will look at it they will see putting multiple algorithms together to solve a problem in a non obvious way is in a way no different then putting a bunch of smaller components together to create a new device. I don't believe patenting either really helps promote innovation. (I'm pretty much anti all patents).