The strongest threat toward Microsoft’s revenue is Linux.

Any consumer who is running Linux on a desktop isn’t going to use Microsoft Office, can’t leverage the features of Internet Explorer and Windows Media Player. Beyond an Xbox, it’s unlikely that a Linux desktop user will pay for any Microsoft products or services.

Any IT department that’s running Linux on servers isn’t going to use SQL Server, Exchange Server, Sharepoint Server or BizTalk Server, and is unlikely to want to use Microsoft’s nascent SaaS offerings.

By contrast, a consumer that’s using Windows on the desktop is a potential revenue goldmine. So, too, is an IT shop that’s running Windows on the server. Even if that shop is using WebSphere, WebLogic, Oracle, Sybase or SAP, if it’s running on Windows there’s still revenue flowing to Microsoft, and the potential for migrating that user over to the Microsoft stack. But if they’re on Linux, Microsoft’s battle is much harder.

One of Microsoft’s strongest weapons against Linux (and against Mac OS X and Solaris, which are growing threats on the desktop and server, respectively) has been software compatibility. Windows stuff just isn’t compatible with non-Windows stuff. OpenOffice isn’t 100 percent transparently interoperable with Microsoft Office. Alternative email clients, like Thunderbird or Eudora, aren’t 100 percent interoperable with Exchange Server. (Neither is Microsoft Entourage for the Mac, for that matter.) Many of Microsoft’s SaaS services require Internet Explorer. Non-Windows enterprise desktops and servers don’t play well with Active Directory.

None of this is news, of course, to users of non-Microsoft operating systems, who have to spend a significant amount of time working on compatibility issues. And it seems as if it should always be Microsoft’s strategy to ensure that Linux solutions aren’t 100 percent interoperable with Windows.

In that light, how should one interpret Microsoft’s deal with Novell regarding interoperability collaboration with Novell? (There was a separate agreement regarding patent licensing, which is a topic for another day.) Simply put, it means nothing good for the Linux community.

The announcement says that the companies will work together on virtualization, Web services management and document format compatibility. The companies were both very short on specifics, beyond talking about a combined offering that will let SUSE Linux Enterprise Server run inside a VM on a Windows Server.

Are we going to see Microsoft release tools to make Windows Servers more interoperable with Linux servers in the data center, beyond some Web services work? No. Are we going to see any Microsoft applications running on Linux desktops or servers? No. Are we going to see features added to Windows Server that help non-Windows clients to work with them, such as on authentication, using SharePoint Portal Services, working with Exchange Servers or ASP.NET? No. Office Live? No.

Big picture: This announcement doesn’t mean that Microsoft likes Linux or supports Linux. It just means that Microsoft found a way to make some money off it, and maybe also fragment the community at the same time.

Z Trek Copyright (c) Alan Zeichick