Windows server and Linux are the two most prevalent server operating systems in use today and there are passionate proponents of both.  It’s not my intent to enter into a religious debate on the windows vs linux issue.  The following windows vs linux table is a bottom line breakdown of the features available to each:

From the above Windows vs Linux table it is clear that there are more similarities in features than differences between the two server technologies.  One factor not mentioned above is price - Linux is cheaper to license than Windows and Windows web hosting packages typically reflect that cost.

As noted elsewhere, FTP allows the uploading and downloading of files to and from the web server.  Telnet and SSH allow access directly to the server opening a UNIX command line window.  Though Windows Server permits the protocols very few administrators offer it.  Some Linux servers now support Frontpage although you’ll still see that cited as a major reason to choose Windows Server.  CGI and Perl are offered on Windows but are more commonly found on Linux hosting platforms.  Databases like mySQL and Access allow the creation of dynamic web pages - only Windows servers support Access.

Many people will cite security as a reason to choose Linux over Windows Server but the notable security issues of Microsoft are on the client operating systems and not server OS’s.  Server security is a matter of good administration - both Linux and Windows Server will not protect against a bad administrator.  From my own experience, we use Windows Server on Secret networks across DOD which has extremely rigorous security requirements.

A minor issue that is a feature or annoyance for some is case sensitivity.  Linux is case sensitive about file names meaning that page.html can be one file, Page.html another, pAge.html yet another (you get the point).  Windows treats these as the same file regardless of capitalization.  Care must be taken when naming files in Linux.  It is not uncommon for pages to look fine when viewed on a web browser on your computer as your web page might point to an image called image1.jpg but the image uploaded is image1.JPG.  A linux server would not display the image while a windows server would.  Again, a minor difference, but worth noting.

As far as making a decision, if your requirements drive you to a particular Server OS then you shouldn’t be concerned that you are “missing out” or making a compromise.  Both are feature-rich and secure and will serve you well provided you host with a reputable company.