I agree with Dan Gillmor's FT column on the operating system wars that the Mac OS X is now clearly in front. But I think you have to reach further back into history to analyze the situation in today's market.
Superiority has never been a factor in the OS wars. Applications were, and Microsoft did a better job of wooing the developers. The software more people wanted to run was usually on Windows and not on OS/2 or the Macintosh.
Applications are still king, but there's now a different list of applications-that-matter. The Web browser has been the most important for a long time, but application developers are just getting the hang of creating really compelling software for it. Gmail is one of the best email clients available, and it runs on any operating system with a modern browser. Other earth-shaking applications such as Skype, several varieties of blog readers and Flickr (for photos) are also almost equally useable on Windows, the Mac and Linux. Word processors, spreadsheets and presentation software are still very important, but Microsoft Office runs on both the Mac and Windows acceptably. Even Linux users can use Office-compatible applications that are free and perfectly useable for 90-95 percent of users. The best photo and video editors and music recording software aren't on Windows. Where Microsoft remains in front is on games, but serious gamers use dedicated machines, like the Playstation.
So what's left to distinquish the operating systems? Stability, useability and security. At the moment, on any one of those criteria, Windows is second at best. Microsoft beats the best of the Linux setups in useability, though distributions such as Ubuntu are incredibly close. On stability, the latest version of Windows XP isn't bad, but it still builds up cruft, slows down dramatically over time and takes entirely too much time and effort for maintenance. On security, I don't think the gap is as wide as many people seem to believe, but for Grandma or the average computer-phobic users who just wants to read email and do their homework, OS X and Linux are clearly and strikingly ahead. If you're going to put a Windows computer on a broadband connection, you better really understand what a firewall is and how to work it. Otherwise, get a Mac, or if you can't afford one, get a college student to set up a Linux PC for you. Please.
I also agree with Dan that Microsoft works best when it feels under pressure. But what does it really have that others don't? Its size isn't as much of a factor anymore. Linux and even OS X (which is based on an open-source operating system at its core) has thousands of developers behind it.
Ironically, Microsoft is now on the other side of a battle fought decades ago, when manufacturers of mainframes, unix servers and minicomputers hoped to keep the personal computer at bay by counting on the reluctance of companies to migrate software from one type of computer to another. And look what happened then.
Update: Forbes has done a good story on the problem Microsoft faces.