Both have their merits, so the first thing you should think about when making this decision is if you are looking for stability, or ease of use. UNIX based servers are generally superior in the site up-time and stability areas than Windows systems. However, while they need to be rebooted more often, Windows servers are generally easier to administer and use.

Many beginners to web hosting will be confused over the pros and cons of the different operating systems. While, Unix is more stable and secure it uses a command line interface for administration. This interface, which is like the original MS-DOS interface, can be difficult to understand to a website newbie. Also, in order to keep a UNIX machine stable, one must update the kernel and software regularly, a process which is more difficult than Windows. This however, can be made just as easy to do if your web host has good administration software.

Another thing to consider when choosing which operating system to use is whether you will be using scripting. If so what kind? For example, if you will be using a dynamic site, and decide that you want to go Perl as your language of choice then UNIX should be your operating system of choice. This is also true for languages such as PHP, and Pythlon. On the other hand, if you choose to go for an ASP based site then you should choose Windows. However, to complicate the matter further some UNIX systems can run ASP scripts, although the quality of the script execution can be lesser.

Bare in mind that if you choose a Windows-based web server (this does not apply to hosting accounts as the host should take care of it for you) you will need to update the software with patches from Microsoft's web site almost weekly to prevent your site from being exploited. UNIX administrators will only have to do so monthly or so as UNIX is more secure by nature, and needs fewer patches and software updates.

UNIX operating systems are generally the preferred operating system, however, in the end, if you do everything correctly, a UNIX hosted web site and a Windows hosted web site will function somewhat equally, and both should make you happy. Be sure to keep operating costs and maintained in mind when making your decision and you won't regret it.