Canonical, a company that sponsors many free software projects and is tightly knit with Ubuntu, has apparently also been approached by Microsoft for such a “deal”. Apparently, however, Canonical refuses to talk to them about this, claiming that there is no legal merit and that deals of that nature don't actually help anything:
"Allegations of 'infringement of unspecified patents' carry no weight whatsoever. We don't think they have any legal merit, and they are no incentive for us to work with Microsoft on any of the wonderful things we could do together," he wrote. Shuttleworth said these patent agreements create "a false sense of security" and do not effectively protect the user from a patent suit from a big company like Microsoft.
He also was critical of Open XML, the Microsoft specification that is claimed to be an interoperable standard. He instead praised the existing OpenDocument format, and that Microsoft should work to improve their support for it rather than vice versa. Whether or not Microsoft is pursuing working with Canonical isn't clear, though judging by their voracious appetite for other companies it wouldn't surprise me in the least. If Shuttleworth, CEO of Canonical, sticks to his word, however, it won't be over patent protection.
Hopefully more companies will model this behavior, and stop rolling over for Redmond. In the long run, this only benefits Microsoft and could actually endanger other companies.