This is more serious than originally anticipated. In the Microsoft vs Salesforce lawsuit, Microsoft brought forward nine patents. Those nine patents out of thousands were picked for their strength. After some posturing from Salesforce, Salesforce was forced to settle with Microsoft.
One of the most damaging patents to Linux was the Network Software Update Patent (5,845,077). This covers various shades of updating the installed selection of software with newer versions of the software that might contain bug fixes, security fixes or additional features available on a remote server.
This is a strong patent, as Microsoft filed this patent in November 1995 and the patent was granted in 1998 and predates both Red Hat, and Debian's software update systems.
In November of 1995, Red Hat had just released Red Hat 2.1. Although Red Hat already had the RPM packaging system by then, RPM did not have any network software update functionality.
By the time the patent is granted in 1998, the mailing list archives for Red Hat still indicate that users downloaded updates from FTP, and manually installed those. This continues at least up to 1999. The situation is not better in the Debian world, the design discussions for what would become the APT program were on the design board in 1998 and nothing would be worth showing to the world
Although other technologies were developed later to deal with software updates, both RPM and DPKG are the foundation on which those were built on the Linux world, and network software updates were handled by software layered on top of it. On the RPM world this was done with either using YUM on Red Hat, APT-GET on Debian and its derivatives and even Red Hat's enterprise up2date tool created after they became a public company.
The situation is pretty bad, because the '077 patent is only the tip of the iceberg when it comes to network software updates. The following are other old patents that Microsoft holds on the network software update space (there are many new ones, but these are the ones that Linux would infringe):
System and method for managing and communicating software updates.
Method and system for downloading updates for software installation.
Software updating system and method.
Automatic software installation on heterogeneous networked client computer.
So it might turn out that every Linux system in use today, from Red Hat, to Ubuntu, to CentOS, to Debian, to SUSE, to ArcLinux are all infringing on Microsoft's patents.