As LWN and everbody else reports (prolinux.de here), Microsoft is active on the OS front. From the LWN article:

Microsoft is starting to rattle the patent saber in a more serious way. "But [Microsoft general counsel Brad Smith] does break down the total number [of patents] allegedly violated - 235 - into categories. He says that the Linux kernel - the deepest layer of the free operating system, which interacts most directly with the computer hardware - violates 42 Microsoft patents. The Linux graphical user interfaces - essentially, the way design elements like menus and toolbars are set up - run afoul of another 65, he claims. The Open Office suite of programs, which is analogous to Microsoft Office, infringes 45 more. E-mail programs infringe 15, while other assorted FOSS programs allegedly transgress 68."

While that might well be true, MS so far doesn't seem to specify *which* patents exactly are infringing. It is going to be interesting how that plays out in the future.