Software patents have long been a lightning rod issue in free software, because they pose the only real threat against which the free software community cannot defend itself. Copyright and trademark problems can always be gotten around. If part of your code looks like it may infringe on someone else's copyright, you can just rewrite that part while continuing to use the same underlying algorithm. If it turns out someone has a trademark on your project's name, at the very worst you can just rename the project. Although changing names would be a temporary inconvenience, it wouldn't matter in the long run, since the code itself would still do what it always did.
But a patent is a blanket injunction against implementing a certain idea. It doesn't matter who writes the code, nor even what programming language is used. Once someone has accused a free software project of infringing a patent, the project must either stop implementing that particular feature, or expose the project and its users to expensive and time-consuming lawsuits. Since the instigators of such lawsuits are usually corporations with deep pockets—that's who has the resources and inclination to acquire patents in the first place—most free software projects cannot afford either to defend themselves nor to indemnify their users, and must capitulate immediately even if they think it highly likely that the patent would be unenforceable in court. To avoid getting into such a situation in the first place, free software projects have sometimes had to code defensively, avoiding patented algorithms in advance even when they are the best or only available solution to a programming problem.
Surveys and anecdotal evidence show that not only the vast majority of open source programmers, but a majority of all programmers, think that software patents should be abolished entirely. Open source programmers tend to feel particularly strongly about it, and may refuse to work on projects that are too closely associated with the collection or enforcement of software patents. If your organization collects software patents, then make it clear, in a public and irrevocable way, that the patents would never be enforced when the infringement comes from open source code, and that the patents are only to be used as a defense in case some other party initiates an infringement suit against your organization. This is not only the right thing to do, it's also good open source public relations.
Unfortunately, collecting patents purely for defensive purposes is rational. The current patent system, at least in the United States, is by its nature an arms race: if your competitors have acquired a lot of patents, then your best defense is to acquire a lot of patents yourself, so that if you're ever hit with a patent infringement suit you can respond with a similar threat—then the two parties usually sit down and work out a cross-licensing deal so that neither of them has to pay anything, except to their patent lawyers of course.
The harm done to free software by software patents is more insidious than just direct threats to code development, however. Software patents encourage an atmosphere of secrecy among firmware designers, who justifiably worry that by publishing details of their interfaces they will be making it easier for competitors to find ways to slap them with patent infringement suits. This is not just a theoretical danger; it has apparently been happening for a long time in the video card industry, for example. Many video card manufacturers are reluctant to release the detailed programming specifications needed to produce high-performance open source drivers for their cards, thus making it impossible for free operating systems to support those cards to their full potential. Why would the manufacturers withold these specs? It doesn't make sense for them to work against software support; after all, compatibility with more operating systems can only mean more card sales. But it turns out that, behind the design room door, these shops are all violating one another's patents, sometimes knowingly and sometimes accidentally. The patents are so unpredictable and so potentially broad that no card manufacturer can ever be certain it's safe, even after doing a patent search. Thus, manufacturers dare not publish their full interface specifications, since that would make it much easier for competitors to figure out whether any patents are being infringed. (Of course, the nature of this situation is such that you will not find a written admission from a primary source that it is going on; I learned it through a personal communication.)
Modern free software licenses generally have clauses to combat, or at least mitigate, the dangers arising from software patents. Usually these clauses work by automatically revoking the overall open source license for any party who makes a patent infringement claim based on either the work as a whole, or based on the claimant's code contributions to the project. But though it is useful, both legally and politically, to build patent defenses into free software licenses in this way, in the end these protections are not be enough to dispel the chilling effect that the threat of patent lawsuits has on free software. Only changes in the substance or interpretation of international patent law will do that.
Recent developments, such as the 2014 decision by the U.S. Supreme Court against the patentability of abstract ideas, in Alice Corp. v. CLS Bank (en.wikipedia.org/wiki/Alice_Corp._v._CLS_Bank_International), have made the future of software patents unpredictable. But there is so much money to be extracted via infringement claims, in particular by patent trolls but in general by any entity with a large patent portfolio and a lack of other revenue sources, that I am not optimistic this fight will be over any time soon. If you want to learn more about the problem, there are good links in the Wikipedia article en.wikipedia.org/wiki/Software_patent. I've also written some blog posts summarizing the arguments against software patents, collected at www.rants.org/patent-posts. As of this writing it's been about six years since the main posts there were published, but all the reasons why software patents are a bad idea are just as true now as they were then.
 See groups.csail.mit.edu/mac/projects/lpf/Whatsnew/survey.html for one such survey.
 Remember that a patent may cover, or "read on" in patent jargon, code that the patent owner did not themselves write. It is thus not necessary for a party to have contributed code to an open source in order to claim patent infringement by that project.