Windows and UNIX are in fact two different systems and of course we are referring to computer systems. A web host uses computers, (we shall refer to them as servers, just computers, but sometimes larger) to host websites, and all computers need a operating system, so Windows and UNIX are the operating system.

The Windows used is normally Windows NT or 2000 and of course as you know Microsoft charges for it's software, while UNIX is an open source operating system, this means that the original creators of the system have given up the rights and anyone can use it, change, improve or do anything they want with, free of charge.

From this we already have to main differences, Window hosts are more expensive and UNIX is more reliable, because it as been improved by thousands of anonymous people. Most probably you are reading this in front of your computer which most probably is operates on a Windows XP, have you noticed that it sometimes, it freezes, and the only solution is to restart it? UNIX is much more stable, robust, time-tested, flexible platform for a web server.

But Windows servers have also it's positive sides, they are compatible with Microsoft applications, and fully support Microsoft FrontPage, Microsoft Access and MS SQL, they also offer advance-programming environments and features such as Active Server Pages (ASP), the ASP.NET framework, Visual Basic Scripts, MS Index Server, Macromedia's and Cold Fusion.

Windows operating system require little or no experience in web development to get advanced features working very quickly because of better graphical user interface (GUI) Software such as Microsoft's FrontPage is specially developed for the webmaster to decrease the website development time and efforts.

Lets go back again to UNIX, they support FrontPage, Flash, Shockwave, Real Audio/Video, Cgi Scripts, Perl, PHP, SSH (Secure Telnet), MySQL, Web-Based Control System, Anonymous FTP, Web Site Graphical Statistics, Web-Based Email System, Miva/XML, Cold Fusion Perl, JAVA, PHP, C, C++, Miva, Shell Access and other wide verity of feature like Telnet and SSH that provides lots of flexibility and freedom in managing file and directories, but some of this require advance knowledge of Unix commands in order for you to customize the scripts to match your website needs. Because of the nature of UNIX, (open source) and the people who love it, there is on the WWW freely available software and scripts, again bringing the cost down.

Concluding which one is the best, it really depends what you need, if you need high uptime, security and not so expensive then go with UNIX, if you need to run Windows applications like, MS Access or the MS SQL SERVER then Windows is your choice.