Novell investors may be cheering the Linux vendor's historic partnership with Microsoft, but Linux advocates had an entirely different reaction, expressing concerns that the deal may hint at future patent lawsuits and possibly even violate Linux's software license.

"Excuse me while I go throw up," wrote Pamela Jones, the editor of the Groklaw.net blog, which tracks legal issues in the free software community. "I gather Microsoft no longer thinks Linux is a cancer or communism. Now it just wants a patent royalty."

Microsoft and Novell agreed Thursday to work together on marketing and development of their respective products and pledged to make it easier for Windows and Novell's Suse Linux to co-exist in the data center.

But, included in that announcement is a patent cross-licensing agreement that is raising concerns. As part of the agreement, Microsoft has said that it will not sue noncommercial Linux developers and users of Suse Linux, but some worry that this move leaves the door open for the company to sue other Linux companies or even Linux users.

"This is actually really bad news," said Bruce Perens, a well-known Linux advocate. "It sets up Microsoft to assert its patents against all commercial open source users. The deal is going to be, 'You have to buy Microsoft-licensed Linux distribution from Novell or there is an implicit threat that Microsoft will assert their patents against you."

Perens even questioned whether Novell's patent agreement might violate Linux's software license, known as the GNU General Public License (GPL), which prohibits Linux distributors from obtaining exclusive patent licenses. "Is Novell going to break the GPL, because the GPL says if you offer a patent license, it's for everyone?" Perens asked.

Microsoft has structured its deal with Novell to avoid any conflict with the GPL, said David Kaefer, Director of Intellectual Property and Standards with Microsoft.

The company with the most to lose from Perens's "implicit threat" is Red Hat, the dominant Linux distributor. Red Hat's stock (RHAT) dropped nearly 25 percent the week before on news that Oracle planned to begin offering competing Linux support offerings, and it was down again Thursday on news of the Microsoft deal.

At a press event in San Francisco Microsoft Senior Vice President and General Counsel Brad Smith declined to comment whether Microsoft thought that Novell rival Red Hat's Linux distribution violates Microsoft's intellectual property.

Red Hat executives were not immediately available to comment for this story.

At the Thursday press event, Microsoft Chief Executive Officer (CEO) Steve Ballmer said that his company chose Novell simply because it had put together a workable deal. "We had discussion with lots of folks in the industry, you can probably guess a list of names," he said in response to a question about Microsoft's relationship with Red Hat, "But it was really when [Novell President and CEO] Ron [Hovsepian] called and negotiated a contract... that we were able to put together something that addressed the business issues, the technology issues, and the patent issues all at once," he said.

Corporate users seemed less concerned with the agreement than the advocates.

"This might actually encourage us to move to Linux in the long-run," said Sherwin Lu, director of application infrastructure for Le Petite Academy. The Chicago-based preschool chain mostly runs Windows throughout its back-end, though it runs a number of open-source and Java applications -- most notably Red Hat's JBoss application server -- on top of Windows.

Increased interoperability between Windows and Linux especially helps IT departments overseeing mixed environments, by reducing the need to hire and maintain separate teams of techies with disparate skills, he said.

While advocates like Perens and Jones may be concerned with the Microsoft deal, Linux's best-known spokesman was sanguine. "I prefer to be an optimist, and will happily take the option that not everybody needs to be enemies," said Linus Torvalds, the creator of the Linux kernel in an e-mail message. "Let's see how it all pans out."

Computerworld's Eric Lai contributed to this story.