However, Microsoft’s statement showed its target is the broader Android operating system.

“The Android platform infringes a number of Microsoft’s patents, and companies manufacturing and shipping Android devices must respect our intellectual property rights,” Deputy General Counsel Horacio Gutierrez said in a statement, “To facilitate that we have established an industry-wide patent licensing program for Android device manufacturers.”

Gutierrez said that others, such as HTC, have agreed to license Microsoft patents for use with Android-based products and added that Microsoft “tried for over a year to reach licensing agreements with Barnes & Noble, Foxconn and Inventec.”

A Barnes & Noble spokeswoman declined comment, citing a policy against speaking about litigation matters.

Microsoft has also taken to the courts over Android as well, filing patent suits against Motorola for that company’s use of the Google-developed open source operating system.

Redmond has said that, while it hopes Windows Phone will eventually rival Android in the market, it is seeking revenue for its mobile patents from those making Android-based devices.

“Their refusals to take licenses leave us no choice but to bring legal action to defend our innovations and fulfill our responsibility to our customers, partners, and shareholders to safeguard the billions of dollars we invest each year to bring great software products and services to market,” Gutierrez added.

Late Wednesday, its Motorola Mobility subsidiary slapped Microsoft with a lawsuit accusing the company of infringing 16 of its patents in a variety of products– including Windows, Exchange, Messenger, Outlook, Windows Marketplace, Bing Maps and Xbox.

“[We are] bringing this action against Microsoft in order to halt its infringement of key Motorola patents,” Kirk Dailey, corporate VP of intellectual property at Motorola Mobility, said in a statement. “Motorola has invested billions of dollars in R&D to create a deep and broad intellectual property portfolio and we will continue to do what is necessary to protect our proprietary technology.”

Microsoft, for its part, seems largely unfazed by Motorola’s right-back-at-ya maneuver. Indeed, in a statement, Horacio Gutierrez–Microsoft’s deputy general counsel of intellectual property and licensing–essentially said the company was waiting for it. “This move is typical of the litigation process and we are not surprised,” he said. “We remain confident in our position and will continue to move forward with the complaints we initiated against Motorola in the U.S. District Court for the Western District of Washington and with the International Trade Commission (ITC).”

In dueling complaints against Motorola with the International Trade Commission and federal court in Seattle, Microsoft claims Motorola’s Android phones violate nine patents relating to synchronizing e-mail, calendars and contacts, scheduling meetings, and notifying applications of changes in signal strength and battery power.

We have a responsibility to our customers, partners, and shareholders to safeguard the billions of dollars we invest each year in bringing innovative software products and services to market,” Horacio Gutierrez, Microsoft’s corporate VP and deputy general counsel of intellectual property and licensing said in a statement. “Motorola needs to stop its infringement of our patented inventions in its Android smartphones.”

What does Motorola have to say about that? Not much. The company says it hasn’t yet received a copy of the complaint, but when it does, watch out. “Motorola has a leading intellectual property portfolio, one of the strongest in the industry,” it said. “The company will vigorously defend itself in this matter.”

Here’s a copy of the ITC complaint:

MSFTvsMOTO –

“We are pleased to reach this agreement with Salesforce.com to put an end to the litigation between our two companies,” Microsoft Deputy General Counsel Horacio Gutierrez said in a statement. “Microsoft’s patent portfolio is the strongest in the software industry and is the result of decades of software innovation. Today’s agreement is an example of how companies can compete vigorously in the marketplace while respecting each other’s intellectual property rights.”

Microsoft first sued Salesforce.com in May, alleging the company’s CRM services violated nine Microsoft patents. Salesforce.com promptly branded the company a patent troll and “a former leader of industry.” But a month later, it slapped Microsoft with a patent suit of its own and hired David Boies, the former U.S. Justice Department attorney who successfully argued the federal antitrust case against Microsoft, to represent it.

“I guess you know you’ve made it in software when Microsoft is protesting your event. Or maybe when they’ve sued you. This is the greatest thing that’s ever happened in my career.”

– Salesforce.com CEO Marc Benioff

Salesforce.com CEO Marc Benioff says Microsoft is a patent troll. Looks like it takes one to know one. On Thursday, the company answered Microsoft’s charges of patent infringement with patent-infringement charges of its own.

In a suit filed in U.S. District Court in Delaware, Salesforce accuses Microsoft of willfully violating five of its patents and using them in everything from Windows 7 to the Windows Live authentication system. And the company is really going for the neck here: Not only is it seeking triple monetary damages, it has hired David Boies, the former U.S. Justice Department attorney who successfully argued the agency’s antitrust case against Microsoft, to represent it.

But if Microsoft (MSFT) finds this disconcerting, the company isn’t letting on. Reached for comment, Horacio Gutierrez, vice president and deputy general counsel, said it’s still intent on taking Salesforce (CRM) to the mat over this. “We are reviewing Salesforce.com’s filing, which we have just received,” he said. “We remain confident about our position and will continue to press ahead with the complaint we initiated in the U.S. District Court for the Western District of Washington.”

“We continue to analyze the potential merits of their claims, the potential defenses to such claims and potential counter claims, and the possibility of a license agreement as an alternative to litigation,” the company said. “However, there can be no assurance that this claim will not lead to litigation in the future.”

Well, looks like the claim has indeed lead to litigation, and litigation from a formidable opponent, too: Microsoft (MSFT).

On Thursday, the software behemoth filed suit against Salesforce, accusing the company of infringing nine patents describing things like “Method and system for stacking toolbars in a computer display” and “System and method for controlling access to data entities in a computer network.”

The complaint, filed in U.S. District Court in Seattle, seeks an injunction against Salesforce and unspecified monetary damages.

“Microsoft has been a leader and innovator in the software industry for decades and continues to invest billions of dollars each year in bringing great software products and services to market,” Horacio Gutierrez, Microsoft’s deputy general counsel of Intellectual Property and Licensing, said in a statement. “We have a responsibility to our customers, partners, and shareholders to safeguard that investment, and therefore cannot stand idly by when others infringe our IP rights.”

An interesting move for Microsoft, which doesn’t typically initiate patent litigation. Though it has been sued many times for patent infringement over the years, the company has only filed a handful of IP suits itself.

That said, Microsoft and Salesforce have been competing more aggressively in the cloud-based CRM space recently.

Salesforce.com declined comment on the suit.

Android may be Open, but evidently it’s not quite “free.”

According to Microsoft (MSFT), smartphones running Google’s (GOOG) mobile OS infringe its patents and companies who use it owe it royalties. Late Tuesday night the company issued a statement announcing a patent licensing deal with HTC that provides the Taiwanese cell phone “broad coverage under Microsoft’s patent portfolio for HTC ‘s mobile phones running the Android mobile platform.” The agreement applies to all Android-based phones made by HTC — including Google’s Nexus One. Financial terms weren’t disclosed, nor were the patents at issue here, but sources close to the company tell News.com that Microsoft believes Android’s infringement of its IP is fairly broad, ranging from the user interface to the guts of the OS itself.

If that is indeed the case, we may soon see Microsoft negotiating similar deals with Motorola, LG, Samsung and other Android handset manufacturers. And that is very clearly the end game here according to a statement from Horacio Gutierrez, the company’s deputy general counsel of intellectual property and licensing.

“Microsoft has a decades-long record of investment in software platforms,” he said. “As a result, we have built a significant patent portfolio in this field, and we have a responsibility to our customers, partners, and shareholders to ensure that competitors do not free ride on our innovations. We have also consistently taken a proactive approach to licensing to resolve IP infringement by other companies, and have been talking with several device manufacturers to address our concerns relative to the Android mobile platform.”

We have been talking with several device manufacturers to address our concerns relative to the Android mobile platform.

In other words, this is the first such deal covering Android, but not the last. So, who will be next?

And how ironic is it that handset manufacturers who opt to use an open Google OS must pay Microsoft to do so?

One last point worth making, here. HTC’s patent licensing deal with Microsoft comes as the company girds itself for battle with Apple (AAPL) which sued it for patent infringement last March. In that suit, Apple alleges that HTC infringed some 20 patents related to the iPhone’s graphical user interface, underlying architecture and hardware. Since Microsoft hasn’t disclosed the patents it’s licensing to HTC, it’s difficult to determine if they might provide HTC with a bit of defense in its fight with Apple. We’ll see, I guess.

Google declined comment on the deal.

If that truly is the case, how can Microsoft possibly enforce them? After all, Linux is the creation of a vast community of developers. Pursuing its members would be like … well, like the recording industry suing its customers. Which is obviously possible, but one would think Microsoft would be a bit smarter than that. And, of course, it is. Which is why it’s seeking licensing deals from those with deep pockets and a serious aversion to risk: Linux’s major corporate users.

“Gutierrez and Microsoft aren’t interested in intellectual property rights,” said VA Software founder Larry Augustin. “They’re not interested in allowing the open source world to defend itself. They’re not interested in a fair fight. Like a bully, they refuse to face the open source world in a fair fight, instead hinting at willful infringement and making backhanded threats. Why? Like any bully they fear that when faced with a fair fight in the light of day they will be revealed for the bully they are. Like any bully they fear that which they threaten. If Microsoft believes that free and open source software violates any of their patents, let them put those patents forward now, in the light of day, where we can all evaluate them on their merits. If not, then stop trying to bully customers into paying royalties to use open source. It’s time for Microsoft to put up or shut up.”

If that truly is the case, how can Microsoft possibly enforce them? After all, Linux is the creation of a vast community of developers. Pursuing its members would be like … well, like the recording industry suing its customers. Which is obviously possible, but one would think Microsoft would be a bit smarter than that. And, of course, it is. Which is why it’s seeking licensing deals from those with deep pockets and a serious aversion to risk: Linux’s major corporate users.

“Gutierrez and Microsoft aren’t interested in intellectual property rights,” said VA Software founder Larry Augustin. “They’re not interested in allowing the open source world to defend itself. They’re not interested in a fair fight. Like a bully, they refuse to face the open source world in a fair fight, instead hinting at willful infringement and making backhanded threats. Why? Like any bully they fear that when faced with a fair fight in the light of day they will be revealed for the bully they are. Like any bully they fear that which they threaten. If Microsoft believes that free and open source software violates any of their patents, let them put those patents forward now, in the light of day, where we can all evaluate them on their merits. If not, then stop trying to bully customers into paying royalties to use open source. It’s time for Microsoft to put up or shut up.”