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These two operating systems both can support HTML, Cold Fusion, and Java files. It was necessary in the past to use Linux for FrontPage creation but is now easy to use Windows for the incorporation of CGI and Perl as these platforms are easily supported by Windows even though Linux is still more commonly used to support PHP, where Windows uses ASP.
In addition, Security, programming languages, and more all differ between Linux and Windows. But it's a great coup for Linux to note that, if anything, the functionality available for Linux meets and often exceeds that provided by Windows, making one's choice less about operating systems and more about the Web host's other services. It is better to pick a Web host based on its features and services rather than on what operating system is running on its Web servers, as the difference between the two is very little. However, if your Web site particularly requires a certain language due to the programmers you work with, it would be prudent to check for system compatibility before subscribing to a Web host.
Linux supports a wide range of software, applications, languages, and databases such as PHP, Perl, PostGre, MySQL, PostgreSQL and many others making it very scalable. On the downside, Linux is not fully compatible with some Microsoft technologies so if you are using Access, ASP, MS SQL, or VB development tools then Windows would be a better bet.
For most users it would be Linux. Windows hosting is quite a niche market as it is usually the big businesses or some specific softwares that require it. Linux is the most commonly used OS in web hosting environment, especially for end-users. Unless you plan on targeting Windows hosting customers, I recommend reselling Linux web hosting.