Like the EU, they are banning patents on computer programs "as such". A very large fraction of software patents are not patents on computer programs "as such".
An abstract of the report from the GAO website itself, worth reading as a TL;DR:
The really interesting news here is that the report found that "troll" related lawsuits are actually a minority of patent litigation, somewhere around 20%, and that is despite a sharp rise in the recent years.
The EFF  makes a good point that this data does not look at non-litigation trolling preying on small entities and unrelated businesses, a la Lodsys, that extract payment simply through the threat of litigation. (Note that the EFF headline is also not the best representation of the report.)
However, such operations have typically attracted media attention. There have been many, but the first I recall reading was of Fotomedia, who sued anyone that had photo sharing on their website. That was a miniscule operation compared to Lodsys, yet it made news. (Ars Technica tracks a few such trolls. It has not yet covered this report, even though the OP has been a regular Ars contributor.) For now, I find it hard to believe that there are enough of these operations to change the GAOs conclusions.
The other interesting observations are:
1. the rise in litigation, troll-related or otherwise, is attributed in part to the recent changes in patent law, specifically, the AIA. What this report, and many other studies in the area, miss is that even older decisions [2, 3] have had similar effects, something I have previously pointed out using another throwaway account.
2. companies are realizing patents are something that can be monetized rather than just being used to protect ideas.
The OP glosses over all this and talks about vagueness in software patents, which is something I partially agree with. (Specifically, I believe patents being issued after the ~2004 - 2005 have much narrower claims.) However, it's not something that is endemic to software patents. The Doctrine of Equivalents  means that any element in any claim of any patent can be interpreted to cover other ways to implement it as long as it performs the same function. For instance, if the claim mentions using email, but somebody does it using SMS, it may still infringe if the main function is sending a message or notifying a user. However this, in turn works against the patentee when prosecuting patents at the USPTO, because examiners then apply the "broadest reasonable" interpretation of claims to find more and more prior art.
2. Michael Donovan, "The Impact of MedImmune, Inc. v. Genentech, Inc.and Its Progeny on Technology Licensing," http://digitalcommons.pepperdine.edu/cgi/viewcontent.cgi?art...
3. Sara Jeruss, Robin Feldman, Joshua H. Walker, "The America Invents Act 500: Effects of Patent Monetization Entities on US Litigation," http://papers.ssrn.com/sol3/papers.cfm?abstract_id=2158455
Don't get me wrong -- I care about this issue, but I'm curious why would you expect people outside the tech industry to care much?
And here we have a study by a branch of the US Congress, the one entity that, based on the constitution, can make sweeping changes to the patent system. The Congress' investigative branch went off to study the problem and essentially said trolls are not a big problem.
But as far as tech media patent-related reporting goes, this one has gone nigh unmentioned. Even though software patents are specifically called out. Why?
My suspicion is that the lack of attention is mostly because the study does not gel with the perception the tech media is trying to sell, that trolls are a huge burden on the economy. And typically, these complaints are made by practicing companies who, if one were to be uncharitable, one could say are actually doing most of the litigation .
To me, the signs point to a submarine . And if that seems far-fetched, consider this:
You ever hear of a "study" that claimed trolls cost the economy something like 29 billion (pinkie to corner of mouth) dollars a year? A number that gets mentioned in any article about trolls or patents in general? Well, last year multiple sources poked holes all over it [3, 4, 5, 6].
Would you like to guess how many tech media outlets reported about that?
Now, would you also like to guess how many tech media outlets continue to harp on about the debunked 29 billion number every chance they get?
5. (Pay-/Registration-walled) http://www.iam-magazine.com/blog/Detail.aspx?g=454c1adc-52c3...
6. (A recap of the previous 3 references, as well as highlighting the sources of funding for the authors of the "study") http://gametimeip.com/2012/07/30/patent-scholars-challenge-b...
Who profits from software patents? Who gets held back?
Why does the narrative matter at all? Don't you remember the fucking shit throwing contest over pinch to zoom?
What drugs are you taking. Are they legal?
That is the only question that matters (beyond just "software" patents,) And there is a lot of work by a lot of people that try to answer the question. Search ssrn for work by authors like Risch, Merges, Allison, Lemley, Mann, Zeidonis, Etro (just for starters) and you'll see that the issue is much more nuanced and complex than what the common narrative tells you.
So does the narrative matter? Well, let's look at the rest of your comment.
You mention a "doubly linked list" patent. That patent is not the greatest ever, but it is not a doubly linked list:
(Note that even the highest rated answers there get it slightly off.)
Then, pinch to zoom; I'm not sure what you refer to by that, but the last time Apple's patent was mentioned on HN, its scope was also grossly misrepresented.
Your reply makes two things clear:
1) you have strong emotions about this topic; and
2) you don't really understand how these things work.
And seeing other comments on HN over many years, I can safely extrapolate another thing:
3) your condition is common to the vast majority of commenters here.
At least to me it seems clear why the narrative matters.
a). A data structure is patented. I'll give you that it's not a doubly linked-list, but seriously. If we are going to start claiming modifications are unique enough for a patent I guess I should probably look into copying some n-array.
That patent is for zooming and making the UI 'bounce' as though somehow that is an amazing and ingenious idea. No, it's not. Just because I'm too stupid too invent an iPhone does not mean I couldn't have invented that in less than a week.
I do have strong emotions about this topic! When a company infringes on the hard work of others I think it's a real fucking big deal. When tripe shit gets media attention and takes years to settle, it just fucks over everyone with a real patent.
Listen, I agree with the Rearden steel narrative. But if we are going to let any fucker who can fill out a patent application get dibs on a goddamn data structure, well you can go fuck yourself. I'd rather be a damn hermit at that point.
a. Can you make a logical argument why data structures should not be patented, as opposed to, say, mechanical or electronic structures? Try to differentiate them using concrete, technical reasons rather than handwavy "software is math" (aka "mechanisms are just physics" or "electronics are just flowing particles") arguments.
Also, modifications have always been patentable ("a better mousetrap" etc.) The thing is, this patent is not even a straightforward modification; I still have not figured out a solid reason why anyone would use this, a single multiply-ordered linked list, over multiple differently-ordered linked lists.
b. That's not the "rubber banding" patent you linked, that's the "pinch-to-zoom-if-touch-input-is-multi-point-else-scroll" patent. Anyway. You could argue both of those are bogus patents, but you have the benefit of hindsight. Hindsight is a very powerful bias, which is precisely why US (and most other places) require examiners to provide concrete proof, in the form of dated, published documents, of non-novelty or obviousness to deny a claim. This is, as far as I can tell, the only way to truly objectively quantify a claim's contribution, and this is why you see the patents you see.
Not saying it's a perfect system, but once you decide that patents should be a thing, I personally can't think of a more objective one.
Also, if you think it's as easy as "fill out a patent application to get dibs on something", I strongly encourage you to give it a shot. Assuming a micro-entity status in the US, it should cost you a couple hundred bucks.
The Doctrine of Equivalents is one of the things that make patent law so ridiculously unclear. But there is something more there which is uniquely problematic with respect to software patents.
It seems like the problem is that the vagueness created by the Doctrine of Equivalents at the level of individual claim elements is allowed to expand to the entire claim in software patents, because the claims are allowed to be so abstract that they aren't tied to any particular implementation. So we get patents that claim all methods of achieving a particular outcome rather than being limited to some subset that the patentee ostensibly invented.
The problem with software is that the alternative would break the patent system the other way, because there are so many reasonable alternative implementations of any given abstraction that a patent on any one of them would be effectively worthless (or just equivalent to copyright) since any decent engineer would easily be able to work around it. Which is why just abandoning software patents makes more sense.
Or for electronics patents, you could use any of a thousand combinations of various passive or active components to achieve the same electronic properties.
Or for drug patents, you could deliver the "active" chemical compound in any of a thousand different coatings.
For patents, the specific implementation has always been a secondary consideration (to be precise, for "enablement"), as long as the true "essence" of the invention is protected.
It may seem that it's only in software that all ways of achieving an outcome get encompassed by claims, but this may be due to 1) the prevalence of software patents in litigation these days (as evidenced by the GAO report) and 2) the propensity of tech media to trivialize all patents to soundbites without regards to the actual claims, and then proclaim them to be broad and vague.
Note that broad and vague patents do exist, in many fields, including software-related inventions. However, in my experience, they are not as widespread as it may seem and, as I said before, getting such broad patents is becoming harder and harder, and has been so since the mid '00s. I don't know what to attribute this to, but one of my hunches is the availability of Google search.
That's not really what I'm talking about.
Maybe an example would help. Suppose you're the first to invent disc brakes and you get a claim something like this:
A device for decelerating a vehicle comprising:
a rotor affixed to a rotating axle of a wheel;
a stationary brake pad; and
a hydraulically actuated caliper compressing the brake pad against the rotor.
So now you want to talk about doctrine of equivalents and say that it doesn't matter what material the brake pads are made of, and maybe you're still covered if the calipers are pneumatic instead of hydraulic, etc. Fine.
The problem is that software patent claims don't look like that. The equivalent ends up looking something like this:
A method for decelerating a vehicle comprising:
an interface allowing a user to request deceleration;
a means for converting kinetic energy into thermal energy; and
engaging said means for converting kinetic energy into thermal energy when deceleration is requested in said user interface.
Do you see the difference? The latter covers disc brakes, it covers drum brakes, it covers drag car parachutes, engine braking, dragging a stick against the ground etc. etc. It covers implementations that have exactly nothing to do with the patentee's invention other than employing the same law of physics in their operation in order to achieve the same result.
The way the patent system normally deals with this is that because the second claim covers everything, it doesn't get granted because of prior art. You can't invent disc brakes and get the second claim because drum brakes already exist. The trouble comes when the problem being solved is itself novel, because there is then by definition no prior art solution, so the first person to get to the patent office can get a patent on every possible solution by proposing any possible solution (even if their implementation sucks), since any solution gets you enablement and there is no prior art to invalidate the exceptional claims.
So that's half of the issue. The other half is the zero reproduction cost of computer software. Once a problem is solved it's over. You have a good solution and the solution costs nothing to copy infinitely, so soon everyone has the good solution and further solutions to that problem are no longer anywhere near as interesting. In consequence software development is dominated by the process of creating solutions to novel problems -- exactly the scenario that the patent system allows the first mover to massively over-claim. Hence the enormous trouble specifically with software patents.
For New Zealand to add software patents back in would require back tracking and quite a loss of political capital.