There are some inherent advantages/disadvantages that can be attached to these base environments. Often it comes down to the familiarity of the team with the related technology that becomes the deciding factor differences being not very significant. One big argument in favor of Linux servers is that they cost very little. Even if you include support from companies like Red Hat, it still costs very little. However, you should be aware of the implications of open source licensing issues.
There's one noticeable set of differences between the three operating systems. Comparatively Windows has gone through haphazard development and vulnerabilities keep coming out. UNIX has had a much more disciplined development. Linux has a horde of willing developers who work constantly on patching and updating the basic OS as well as the derived software.
Top of the chart consideration should be given to security. We talked about secure servers in the earlier section, but, generally speaking, Windows is a more vulnerable system security wise than Linux environment.
Access to the websites is typically via FTP only in case of Windows while the UNIX and Linux based systems allow telnet and SSH access too. These allow the files on the server to be manipulated directly. That is more flexible.
HTML is a basic need of any website. But, today you need support for dynamic pages or specific HTML script being generated based on user inputs. Javascript, CGI-Perl, PHP, ASP and ColdFusion are the means to create such facilities and your base needs to support them. Typically ASP works in the Windows environment and PHP works in Linux. ColdFusion is supported on either.
MySQL database has become standard in Linux environment while SQL Server fills that need in Windows. Access to some extent is in use in the Windows set up. Depending on your database requirements you may want to use one or the other.