Linux and Windows are the two major Web hosting operating systems. Traditionally Linux was the first operating system to be used in Web hosting but Windows is catching on quickly. Both operating systems have their pros and cons and as you have probably guessed, in some cases one of them is the better choice, and in other cases it is just the opposite.
The choice between Linux hosting and Windows hosting is strongly affected by personal preferences of the one making the choice. Linux and Windows are two major operating systems - one of them (Linux) is open source, while the other (Windows) doesn't share its source code with the world. Both camps have their supporters and to some extent it is true to say that the discussion if Windows or Linux web hosting is better is a "religious" debate about open source vs proprietary software in general. In a sense, the dispute Windows vs Linux web hosting is like the brunettes versus blondes dispute - both contenders have pros and cons and it is largely a matter of personal preferences.
Anyway, in order to help you make an informed decision about Linux and Windows web hosting, we'll try to summarize some of the main points to have in mind before you make the decision:
Do your applications demand OS or the other? One of the most important issues to consider when choosing Windows or Linux web hosting is what applications you will run on your server. Many applications can be run on both Windows and Linux and some applications are only made for one of the platforms and ported for the other. Still there are cases, when the applications you plan to run are a limitation and they force you choose Linux or Windows.
Even if your applications are ported from the other operating system, generally these applications work best in their native environment - i.e. Apache on Linux, .NET on Windows, so if you are tied to a technology, actually your choice (fortunately or unfortunately) has already been made. In any case, you need to make sure in advance which operating system your applications demand because migrating a site later is not fun.
Is security vital for you? There is hardly a web master, who will say that he or she doesn't care about security. However, in some cases security is especially vital and you can't afford to make compromises with that. Generally speaking, Linux is considered to be more secure (especially the security-enhanced distros) but Windows can also be secured well, if the administrators know their job. So, in terms of security there is no clear winner - you can have Linux and a poor administrator and this is more of a security risk than Windows and a real pro to administer it.
Price. As a rule, hosting packages that use Linux are cheaper and this is not at the expense of quality! Linux hosting packages are cheaper because Linux is free, while Windows costs money and your hosting provider has to charge you a few cents/dollars more because of the licensing fee he or she has paid for Windows. However, all equal, in most cases the difference in price due to the operating system used is quite negligible and it is hardly a critical factor.
Training. Another thing to take into consideration is the ease of use. In the case of Windows vs Linux web hosting, the difference is also negligible. Whatever you choose, the learning curve for you won't be much different. If you are using Windows as your desktop operating system, don't panic about if you choose Linux, that you will have to learn tons of new things - more often than not you will be using Web-based applications to access your site, so whatever operating system you pick, these applications are more or less the same (actually, chances are that you will be using mainly a web browser and/or a FTP client to access your site).
Your test server. Another limitation you might have in your choice between Linux and Windows web hosting comes from the operating system of your test server. It is really wise to have a test server, where you deploy your changes and test them prior to uploading them to your live site. If for some reasons you can't get a test server with the operating system of your choice (for instance, your company regulations dictate that you only use Windows), then this is also a limitation. However, unlike applications tied to one operating system, it is easier to find a workaround to this problem - if nothing else is possible, you could set a test server with the operating system of your choice at home and connect remotely to it to test your changes.
Your personal preferences. Finally, one more pro/con you need to take into account, are your personal preferences. We have already mentioned that the dispute if Windows or Linux is better as a web hosting operating system is not exactly a rational one (except for the applications/technologies, which run only on one of these operating systems), so your personal preferences could be the strongest pro/con in the decision-making process.
Are you confused regarding which one that is the better choice? Don't be - there is no clear answer to this question! Actually, in most cases it doesn't matter if you choose Windows or Linux as your web hosting platform - what matters more is that you choose a reliable provider with little or no downtime, good bandwidth, and affordable (which doesn't necessarily mean low) prices. If your applications/technologies don't force you to choose Linux or Windows, whatever you pick, is a good choice!