It is difficult to find organizations that officially speak up against software patents. There are many that should do so but are under the control of large corporations.The leading organization against software patents is the Foundation for a Free Information Infrastructure (FFII). Without the efforts of the FFII, software patents would probably have been legalized in Europe quickly. The FFII is focused on the ongoing legislative process in the EU. It has achieved such a level of success and notoriety that it is probably the leading organization of software patent critics on a worldwide basis.
The largest industry association that fights against software patents is the CEA-PME group, the members of which are SME associations from 19 different European countries. All in all, CEA-PME represents 500,000 enterprises. On this page you can see which organization in your country is a part of CEA-PME. The members of CEA-PME are usually better known than CEA-PME itself, especially in their respective countries.
Free and open-source software organizations are usually, but not always, against software patents. Unfortunately, large corporations have tried to create free and open-source software organizations that support software patents. You therefore have to be careful. The Free Software Foundation and its European arm are clearly against software patents but there is no certainty about everyone who claims to have some form of involvement with them.
For the most part, the EICTA group of industry associations wants software patents. The German part of EICTA, a group named BITKOM, pretends to be against software patents but actually lobbies for them. However, there are some member associations that have already expressed their dissent from EICTA's position. The patent policy of EICTA and some of its key members, such as BITKOM in Germany, is tailored to the special interests of a few large corporations that are particularly influential there.
It is strongly recommended that you take a look at our discussion forum on this website to learn about where various associations stand. The positions of some organizations may change over time, and in the forum we'll always discuss their latest statements and actions in the context of software patents.