It depends entirely on the patent and the allegations of infringement. Section 101 is something that can be invoked early in a case, so for a software patent that's usually something you want to do. The other two are generally invoked at trial, or possibly at summary judgment before trial (if the evidence is so strong that there is no reason to have a trial).
So if I think about it correctly, there are three ways to dismiss it.
1) Invalidate the patent on the basis of novelty (101).
2) Invalidate the patent of the basis of the prior art.
3) Invalidate the claim on the basis of non-infringement.
[ Am I missing something? ]
Which one do you think is the best strategy (with the most chance of success? Or based on your experience, what will likely work.