David Gerard wrote:
(The EFF is unlikely to be as strident about software patents as the FSF is, because software patents don't affect free speech quite as directly as they affect free software.
Perhaps not now but the threat has already been established: the Heckel-Apple story describes the threat rather well. Stallman tells this story in his patent talk. He's given this talk many times and it is transcribed in multiple locations. This quote comes from http://www.gnu.org/philosophy/stallman-mec-india.html
Few years ago an engineer in US named Paul Heckel was suing Apple. He had a couple of software patents in the late 80's for a software package and then when he saw hypercards and looked at inside — this is nothing like my program. He didn't think any more of it. But later on his lawyer explained to him that if you read this patent carefully hypercards fell into the prohibited area. So he sued Apple feeling this is an opportunity to get some money. Well once when I give a speech like this, he was in the audience, and he said “oh no that's not true. I just wasn't aware of the scope of my protection” and I said “yeah, that's what I said”.
In his talk from 2002-03-25 he elaborated on the threat to computer users -- from http://www.cl.cam.ac.uk/~mgk25/stallman-patents.html
All software developers are threatened by software patents and even software users are threatened by software patents. For instance, Paul Heckel, when Apple wasn't very scared of his threats, he threatened to start suing Apple's customers. Apple found that very scary. They figured they couldn't afford to have their customers being sued like that, even if they would ultimately win. So the users can get sued too, either as a way of attacking a developer or just as a way to squeeze money out of them on their own or to cause mayhem.
The patent laws in the US allow this to happen. This threat exists for all computer users.
And the solution is clear: end software patents.
Critiquing a corrupt system by invalidating "bad" patents ends up preserving, even bolstering, the status quo; the implication is that there are only a few bad actors in an otherwise just and right-minded system so it makes sense, from that unrealistic perspective, to weed out the so-called "patent trolls" and "bad patents". Any critique aimed at increasing scrutiny of patent applications or issued patents (such as Microsoft's critique) will not help the computer users in countries that allow software patents.
Therefore I don't see why the FSF or its sister organizations would champion Microsoft's side in this dispute. Perhaps this is a good opportunity to again speak against software patents and explain why Microsoft's side is merely tinkering with the edges of a horrible system.