This depends on your requirements. If you use PHP, Perl or mySQL with your website, then a Linux distribution would be the most suitable. If you use ASP and/or MS SQL, then Windows is the obvious choice. These constraints aside, Linux has the advantage that (except for Red Hat Enterprise) it is free, where as Windows comes with a monthly license fee. If you decide that you'd prefer to have a GUI to administer your sites with, then a Linux server with Plesk is still the cheaper (and more popular) option.
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