I think it is reason enough to disallow software patents that the system is so extremely abusable and that the incentive to abuse the system is extremely high. The abuse: Throwing the book at the patent office. A massive landgrab in ideaspace. There's just no chance that patent offices anywhere will be able to properly evaluate all patent claims and momentum being what it is patents will most likely be awarded not discarded by default in lieu of a proper examination.
A good case in point is the XML serialization patent story - patent flip-flopping software behemoth Microsoft has done the equivalent of patenting the wheel in patenting, successfully, XML serialization of objects.
Not only is there plenty of prior art that will eventually lead to the patent being discarded, but at a deeper level, that's pretty much what XML is from a certain point of view.
The morale of the story is obvious: It doesn't really matter that the patent will hopefully be discarded at some point, the friction it has already created wil slow evolution of software. Absolutely no invention of anything was protected by the grant of this patent.