The major difference is the server's operating system. You could use Linux to host PHP and MySQL applications and Windows to host ASP.NET and MS SQL apps. Linux hosting is much better compared to Windows and are more stable, less vulnerable and cheaper.
The first difference is the operating system. The following is the price, Linux is open source, available for free, where as Windows is charged for the license. The choice between the two depends on the script to execute in the website. A few scripts like asp, asp.net require Windows and is not compatible with Linux.
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