Honestly (and depressingly) I think the best examples of software patents used for good are the software patents written to protect from exploitation... by the software patent system - i.e. Creative Commons, GPLv2, BSD Licence, ...
I can't think of a good software patent. It's not a software patent, but there was IBM's attempt to patent patent trolling which was a rather keen bit of legal satire. I think it actually failed in the face of all that prior art, but I might be confusing that patent application with another one.