The Unix operating system was made to perform demanding tasks, giving it the ability to run multiple sites on a single machine with ease. It is extremely flexible for programming environments and provides a tremendous level of administrative control. Unix handles CGI scripts perhaps better than any other system, making it ideal for hosting operations that require a lot of automation.
The disadvantages of Unix do not have much of a bearing on end-users or shared hosting customers, but to the server administrator, they can be a determining factor. Thriving off raw DOS-like commands, it can be incredibly difficult to learn as there is no GUI to simplify management tasks. In fact, it can take administrators years to fully grasp all the basic commands of the Unix operating system.
Windows NT was beloved instantly for its ease of use and seamless integration with the FrontPage web authoring tool. This niche variation really appealed to users who lacked the ability to code with scripting technologies such as HTML, CGI and PHP. Despite its popularity, Windows NT quickly gained a bad reputation for being vulnerable to exploits and stability issues. The platform improved greatly with the introduction of Windows Server 2003 and got even better with the release of Windows Server 2008 in 2007.
Windows offers a user-friendly setting that is quite familiar to its desktop environment, making it easier to use for administrators. Instead of complex commands, management tasks can be handled from a GUI boasting icons and easy to use tools.
Now far more stable and secure, the Windows disadvantages have been reduced significantly. The biggest drawback would be cost, which stems from licenses tied to the Microsoft SQL Server, Exchange and even the Windows platform itself.
When it comes down to it, both Unix and Windows have demonstrated their ability to perform efficiently in the web hosting environment. Both are traditionally more expensive than Linux so cost may not be as big a factor as you may think.