Simple
If you run microsoft based programming like asp.net or similar framework that needs windows OS then choose windows server
Else
for all non microsoft scripts / programming or application choose Linux. CloudLinux OS is most stable and reliable.
I have personally hosted wordpress on windows server and linux server. The result shows that Linux is more secure, better performing and reliable.
Let me tell you, if your windows based server is infected with virus, your sites will easily get affected and may get hacked or break soon. In Linux .exe files do not execute at all by default, so from security side, Linux is far better when compared to windows.
For example, if you use wordpress based website, and you uploaded a plugin (infected with malware .exe) file, and it will start executing or spreading inside the server and may affect not only your website, but also whole server. If you install same malware plugin on CloudLinux with ClamAV running realtime, it will stop uploading the plugin itself.
Even if it is uploaded, that malware will not run as it is .exe file, and thus attack is prevented. And during regular scans, we can destroy such malware.
So there are a lot of things to suggest that Linux as better OS for servers.
Choose windows, if and only if you need to host microsoft based programmed websites and applications.
Hope this helps you.
Note:: All the above is based on my personal experience working with thousands of websites and customers over the years. Some people may or may not agree. But this is my personal opinion. Each OS have its own advantages and disadvantages. Choosing a particular OS depends on own requirements and comfort levels.
