Software patents shouldn't apply in the first place, but as they are here now...
If they must exist, they should be as specific as the physical design patents of old. Nothing so general as "A linked list with multiple indicies within itself for alternative list ordering" should ever be patented. My firm belief is that all software patents (if the system continues to have them at all) MUST include the functional source code of their implementation, the commercial or competitive use thereof causing the user the requirement of law to gain license. This source code is referenced in the text of the patent the same way as blueprints or other diagrams are referenced in physical patents. Individuals are legally allowed to recreate any patented work for personal use, to determine for themselves the usefulness of such a device, as long as the device is not distributed. Many new technologies have been built by people creating a new novel device to produce the SAME RESULT of a patented device without using the PATENTED METHOD. Thus, it should be possible to build a different method that does not infringe the patent but produces the same result. This is healthy for technological advancement.
Last time I checked, the patent system was created to give a limited time monopoly to the creator of a novel new device, while preserving such knowledge for the general public to be able to recreate the technology at any point in the future. In recreation, the patent MUST contain enough information to allow someone knowledgable in the field to reproduce the device. In being novel, prior art must not be known. Unfortunately patent researchers typically limit themselves in their search to searching PATENTS for prior art, but if the art was not patented, their search fails to show prior art. Then it becomes a matter of the court, where highly paid lawyers working for wealthy large corporations make a mockery of the original purpose of patent law and squish out of existance many innovative small businesses.
Patents were originally a form of open source for technology, with protection for the originator so that they could profit while still releasing the information for free. I wish that everyone would look at patents that way again.
Standard disclaimers, IANAL, correct me if I'm wrong. Got my opinion researching the patent process for something I invented.