Over the last several years, it has become very clear that the two dominant server operating system environments are Windows and Linux. In fact, it’s not at all uncommon to find both these environments running inside the same organization.

Basically, there are three ways for this situation to come about. The first way is through inheritance, which is usually the result of some merger and acquisition activity in which one side of the deal was primarily running Windows servers while the other favored Linux.

The second, more common, scenario is more ad hoc. At some point, someone on the IT staff brought in Linux servers through the back door, and the application load running on those servers grew over time.

The third and most likely scenario involves a more deliberate strategy whereby the IT leadership has decided to embrace both operating system environments for different types of application workloads.

Most IT organizations chalk up the bickering between the Windows and Linux partisans to good-natured rivalry. But as the economy has taken what looks like an extended turn for the worse, the issue of costs associated with running both operating environments is starting to raise its ugly head.

As a result, the tenor of the Windows-versus-Linux debate is becoming shriller, as advocates for each begin to view the issue as a matter of survival: Many companies must start thinking about standardizing on one environment to reduce costs. The core issue is that each environment requires its own dedicated hardware, management tools and associated specialists.

What could, perhaps, forestall the inevitable is that there are a number of third-party system-management tools that IT organizations can embrace to manage both Windows and Linux server environments. That could reduce the management software footprint in a way that would allow these enterprises to run more systems using fewer people.

But the issue of consolidating servers is trickier. The only way to consolidate Linux and Windows servers on the same machine is to leverage the Hyper-V virtualization technology that Microsoft has made available with Windows Server 2008. As part of Microsoft’s alliance with Novell, the SUSE version of Linux that Novell sells can run as an “enlightened guest” on top of Windows Server 2008. This means that as a guest operating system, SUSE Linux can see and use all the hardware resources that Windows Server 2008 sees and uses.

Unfortunately, Microsoft doesn’t have similar relationships with other providers of Linux distributions. And it’s unlikely that Microsoft is going to allow any of the other Linux providers to run Windows Server 2008 as a guest of Linux any time soon.

So, as a practical matter, if you want to save money by consolidating Linux and Windows servers, you have to take a good, long look at what Novell is doing with Microsoft. A lot of people in your organization might have emotional commitments to other Linux distributions. However, if you want to take advantage of both Windows and Linux in the most cost-effective way possible, the joint offerings from Microsoft and Novell make a pretty compelling case.

Perhaps the best thing about this capability is that it allows an IT organization to save significant amounts of money without forcing the company down one server path or the other. Of course, not all applications lend themselves to virtualization equally well, so it might still be necessary to run stand-alone Linux and Windows servers.

Nevertheless, better than half of the servers could probably run their applications just fine on a virtual infrastructure. And the potential cost savings of uniting Windows and Linux server environments on a common hardware platform are hard to ignore in these difficult economic times.

Consolidating Linux and Windows servers may not be the easiest decision to make, given all the passionate politics involved. And it certainly won’t be the most popular choice. But doing what’s easy and popular is, unfortunately, often the wrong thing to do for the good of the business.