Attempting to ride a wave of corporate and judicial disenchantment with aspects of the current patent system, a new project was unveiled Thursday designed to, as its name bluntly indicates, End Software Patents. (Press release is here. The group’s “first yearly report” on the state of software patents is here.)

The group is intended to become a clearinghouse for information and a hub for those strategizing legal challenges, according to its executive director, Ben Klemens. Though End Software Patents will not initiate litigation of its own, it will be on the lookout for appropriate test cases to support as they arise, he says.

Though the project is being sponsored and funded by leaders of the Free and Open Source Software movement, it hopes to attract support from the wider community of businesses, financial institutions and universities that have all been blindsided in recent years by lawsuits over software patents and their close-cousins, business-method patents.

The End Software Patents Web site, here, highlights a long list of diverse businesses that have been sued for allegedly infringing software patents, including the Green Bay Packers, OfficeMax, Caterpillar, Kraft Foods , ADT Security Services, AutoNation, Wal-Mart , Walgreen , Barnes & Noble, Circuit City Stores , Ford Motor , E I du Pont de Nemours and Co. , and so on. In most cases, the companies have been sued because of certain basic, routine functions performed on their Web sites — the way images are displayed, the way data is gathered or transmitted — which are said to infringe software patents.

The group also hopes to attract support from the many financial institutions, including JP Morgan , Merrill Lynch , and NCR Corp. , that have been asked to pay patent holding company DataTreasury for permission to send check images over the Internet. (For a Washington Post story about remarkable proposed federal legislation directed specifically at the DataTreasury patent, click here.)

The point, explains Klemens, is this: “If you’re running a business of any sort, you have to care about the software and business method patents.” That’s because nearly every business today operates a Web site and employs a staff of in-house IT programmers who enable them to conduct business in the digital age. In that sense, every business is now a software business.

Klemens is a mathematician (a guest scholar at the Brookings Institution since 2003) who uses algorithms to analyze data. In a recent article, for instance, he and his co-authors use data analysis to link certain genes to bipolar disorder. “I often run into patents on statistical methods and mathematical algorithms of the type that I implement,” Klemens says. “I don’t think I violate the ones I’ve seen, but I could be wrong, and I don’t know what else is out there. . . . That’s the thing that really woke me up: by doing pure math, I face legal liability. As far as I know, that’s a first in human history.” Klemens’s personal Web site is here.

In a 2005 book, Mathematics You Can’t Use, Klemens criticizes software patents from an economic and legal perspective, and does so in unusually crystalline, easy-to-understand terms. (For chapter one, see here, and for chapter six, see here.)

The book attracted the attention of the Free Software Foundation, whose president, Richard Stallman, has been railing against software patents since at least 1991, for related, but narrower, reasons: they posed a potentially mortal threat to his brainchild, free software — i.e., software, like Linux, that programmers are able freely to examine, modify, and redistribute without fear that their work will ever be taken out of circulation, declared off-limits, or placed behind a toll-booth by private proprietors. (For a feature story on the tension between patents and free and open software, “Microsoft Takes On the Free World,” see here. Generally speaking, though, software patents present dangerous traps for any programmer. Unlike copyrights, which are difficult to infringe inadvertently, a programmer can easily write software that inadvertently infringes someone else’s patent. That happens whenever the programmer independently comes up with an innovation that, unbeknownst to him, someone else has already staked a claim to. While copyrights are relatively easy to write around — since they protect only particular sequences of words or code — patents present broader, vaguer, and more durable obstacles, since they purport to proprietize implementations of ideas.)

In Klemens, the Free Software Foundation saw a potential ally who, thanks to the breadth of his critique and clarity of his writing, could attract a broader audience than just free and open source programmers. “We came to him,” says Peter Brown, the foundation’s executive director, “and said, we really want to fund your work. And he said yes.”

At the moment, the End Software Patents project is formally an offshoot of the Free Software Foundation. It also enjoys the “sponsorship” — though not monetary support — of the Software Freedom Law Center, which is led by Eben Moglen (an outside lawyer for the FSF and its former general counsel), and of the Public Patent Foundation, an organization led by the center’s legal director Dan Ravicher. The Software Freedom Law Center is itself funded largely by such Linux-supporting corporate patrons as IBM (IBM), Hewlett-Packard (HPQ), Red Hat (RHT), Novell (NOVL), Oracle (ORCL), and Sun Microsystems (JAVA).

To be sure, the goal of abolishing software patents remains a radical position in the sense that very few corporations endorse it. (A surprising exception is pharmaceutical manufacturer Eli Lilly & Co. See here. Evidently Lilly recognizes that poor quality software patents are among the problems spurring the tech industry to seek patent reforms, and it hopes to find of way of placating the tech industry without weakening protections for the drug patents that are the lifeblood of the pharmaceutical industry.)

Though many information technology companies, like IBM, Hewlett-Packard, and Cisco, are publicly championing patent reform, they only favor improving the quality of software patents, not abolishing them. After all, there are estimated to be more than 200,000 active, issued software patents in the United States, and most major tech companies have acquired, at considerable expense, substantial portfolios of them. Companies like Philips Electronics also argue that drawing the line between hardware and software is no longer easy, and that many patents relate to processes that were once accomplished using hardware but are now accomplished using software. Why should the modernization of the medium deprive Philips of recognition for its inventions, its lawyers have argued (albeit, in a slightly different context). See here.

Still, Klemens expects his group to find much common ground with the more moderate IT industry reformers, as well as with those whose main bugaboo is business-methods patents. “Pretty much every argument we make, top to bottom, applies to business methods as well,” Klemens says. In addition, the group’s supporters hope that the major tech players are coming to conclude that the vast number of software patents they have accumulated is part of the problem. “There are so many rights in so many hands,” says Moglen, of the Software Freedom Law Center, “everybody is at risk all the time.”

In any case, even if End Software Patents’ goals are extreme, they are not far-fetched. The U.S. Supreme Court has never ruled on the patentability of software, and at one time the predominant assumption among lawyers was that it could not be, because it amounted to nothing more than mathematical algorithms, which, in turn, were considered nonpatentable “laws of nature.”

That assumption was gradually turned upside down through a series of decisions rendered in the 1990s by the U.S. Court of Appeals for the Federal Circuit, a specialized court that had been set up to handle patent appeals, among other things, in 1984. Those decisions suggested that even if pure software itself was not patentable, software when loaded onto a general-purpose computer created, in effect, a new physical device that could then be patented. Some of the same rulings that opened the door to software patents effectively opened the door to “business method” patents, too.

In the past two years, however, it has become clear to all that the U.S. Supreme Court is extremely unhappy with the patent environment that the Federal Circuit has fostered in the two decades since its creation. In eBay v. MercExchange (May 2006), the Court unanimously junked one longstanding rule of that court, and last term, in KSR International v. Teleflex (April 2007), it unceremoniously dispatched another. (In eBay, the Supreme Court ruled that judges need not always enjoin defendants from infringing, even after a patent-holder has proven its case, and in KSR it made it much easier for judges and patent examiners to invalidate patents due to obviousness.)

For Klemens, however, the most encouraging ruling for his agenda was one that, technically, wasn’t. In LabCorp v. Metabolite Laboratories (June 2006), the Supreme Court had been asked to review the Federal Circuit’s precedents on patentability – the issue that ultimately also determines whether software patents and business-method patents are permissible. After hearing oral argument, the Court punted, deciding that, for technical reasons, it never should have heard the case in the first place. But three justices dissented, writing that they would have overturned the Federal Circuit and invalidated the patent in question, because it clearly amounted to an attempt to patent a nonpatentable “natural phenomenon,” though the phenomenon had been recast in the patent application as a patentable “process.” For that opinion, see here. Klemens contends that software patents amount to much the same thing.

Though only three justices signed the dissent, it does appear that it, in combination with the Supreme Court’s back-of-the-hand treatment of other key Federal Circuit precedents, has led the patent appeals court to engage in some soul-searching. Just two weeks ago, it announced, without having been spurred to do so by the parties, that it would rehear an important patentability case, In re Bilski. (See generally here.) It even asked the parties to brief whether a key ruling it rendered in 1998, State Street Bank & Trust v. Financial Signature Group – one of the pivotal ones greenlighting software and business-method patents — was correctly decided.

“There are test cases all over the place,” observes Klemens. Plainly, his timing is propitious.

Correction:  As a commenter points out, in an earlier version I misused the legal term of art “reads on.” Then I did it again in a comment. Regret both errors.

VMware (VMW) today joins the pantheon of Silicon Valley companies with the audacity to go public not only in the supposed doldrums of summer but in a rotten market to boot. Past honorees: Dearly departed Netscape from 1995 and Google (GOOG), in 2004.

The Palo Alto software shop, a unit of EMC (EMC) burst onto the public markets this morning by trading at $52 after being priced Monday evening at $29. Things have all gone very much as planned for VMware. As I noted in June, anlaysts expected VMware to go public at about $27.  Intel (INTC) and Cisco (CSCO) managed to get in before the IPO, buying sizeable stakes at $23 and $25 per share, respectively.

What’s so great about VMware and August IPOs? Let’s take those questions one at a time.

For all the hoo-hah about new this and new that — read: overhyped Web 2.0 companies you’ll never hear about a year from now — VMware actually solves a problem that matters to big technology buyers. Its virtualization approach allows companies with massive server farms to more efficiently use their server capacity. That simultaneously threatens the big server companies like IBM (IBM), Sun (SUNW) and HP (HPQ) and strengthens the market by making servers more valuable. VMware is the “it” company of Silicon Valley right now, again, among real companies that sell real products. Everyone wants to work with them. The company’s growth has been impressive, far better than that of its parent, whose best move of the past half decade turns out to have been buying VMware. (For the numbers on the growth, see the article I did in the print edition of Fortune; It was called “The next big Silicon Valley IPO.” Sometimes we get it right.)

As for August IPOs, is there some kind of magic? Netscape’s bankers told the company it was folly to go public in the heat of the summer. The company was confident. Google never worried about the month it went public. It fretted more over its auction method. Did VMware plan to do its IPO in August and in the midst of a market meltdown? Certainly not the latter. Still, its success today — and let’s remember, to continue to be a success it needs to keep rising, as Google did, not shrivel like Netscape — is a reminder that 1) there is plenty of capital for quality companies and 2) the markets don’t move in lockstep at all times.

Watch for news from a hot networking company in Petaluma, Calif., called Calix. What you need to know about Calix is that it makes equipment for the Internet TV (known as IPTV — Stephanie Mehta knows all about this stuff) business and is headed by Carl Russo, who made a fortune by selling Cerent to Cisco (CSCO) back in the day. Russo’s a shrewd guy who’s crazy enough to drive race cars and sane enough to pay someone else to fly his private jet.

He was all set to host an analyst day next week at the swanky Four Seasons hotel in San Francisco, a sort of bold move for a private company. I just got an email from Calix’s reps saying the analyst day has been “POSTPONED for now.” That’s almost always a sign of one of two things: that the company is getting ready to go public or has agreed to be sold.

It’s worth remembering that Cerent filed to go public and then sold to Cisco. It’ll be interesting to see if history repeats itself here. (Corey Hajim speculated about a Calix IPO last year in Fortune.)

John McCain was the warmup act Tuesday night at the Wall Street Journal’s D5 technology conference at the lush Four Seasons Aviara in Carlsbad, Calif., north of San Diego. It was my second time seeing McCain in action, the first being at Fortune’s Brainstorm conference in Aspen, Colo., last summer. I like McCain, so I was generally pleased with his performance tonight. I feel like his energy level is down slightly, which isn’t an irrelevant gauge of a candidate’s probability of success. That very likely could have to do with the fact that he spends a fair amount of time discussing a dour and unpopular topic, the war in Iraq, which he continues to support. Still, what’s so appealing about McCain is that he speaks his mind. Over the course of the evening he somewhat won over an largely liberal tech-industry crowd.

I won’t go into McCain’s war policy, though many of us chewed it over during dinner, after his speech. Instead, nuggets about his economic policies:

* McCain is an unabashed free trader. He likes to say that regulations usually bring about intended as well as unintended consequences. He specifically said the 1996 Telecommunications Act, which he helped write, is “irrelevant” today.

* Asked if patent reform is high on his list, he replied, “No.”

* McCain says he’d reach out to successful Americans to get them involved in his admininistration. Asked to name names, he offered up Cisco (CSCO) CEO John Chambers and Microsoft (CEO) Steve Ballmer, both of whom were in the room. To read Roger Parloff’s article in the last issue of Fortune, Microsoft Takes on the Free World, Ballmer probably will be excited to know of McCain’s lack of interest in patent reform.)

* On the subject of immigration reform, McCain again flashed his free-trade credentials, saying, “I worry about nativism and protectionism,” implying he’s more comfortable than most politicians with foreign companies and countries investing in U.S. assets.

Do these political speeches at business conferences translate into votes? Can you picture John Chambers as Secretary of Commerce? Sure.