This eternal question has been debated all over the internet. Unfortunately most of the information you will find is so out-of-date that it's no longer relevant, and it can be hard to find a balanced and objective view.
We're Windows hosts - and have been since 1999 - so we have a slight bias, but we're not blinded by any particular prejudices or misconceptions. With that in mind, let's put a few myths to bed once and for all:
Myth: Linux is more secure than Windows
Once upon a time this may have been true with older versions of the Windows operating system, but over time Windows has become more and more secure to the point where this myth is not only not true, but the opposite is probably true for a default installation. Windows Server 2012 is an extremely secure and safe operating system in it's default installation, and with a good administrator can be made extremely secure.
At the end of the day it's down to the system administrators who looks after the servers. Both Linux and Windows hosting can be extremely secure, with neither Windows nor Linux being better than the other.
Myth: Linux is a more stable hosting platform than Windows
That hasn't been true since the release of Windows Server 2003, and it certainly isn't true with regards to Windows Server 2012. We can say - hand on heart - that we've never had a server running Server 2012 crash, which is also true of all the VPSs that run Server 2012 too. Unfortunately, we can't say the same for some Linux installations who didn't react too well to a network storm and crashed while Server 2012 (and Server 2008 and Server 2003) just kept trooping along.
We've had hardware break, so don't imagine we never have problems, but we've never had an issue with Windows Server 2012. The fact is, you're not going to find a more stable and reliable hosting platform than IIS8 and Windows Server 2012. We're not saying Linux isn't good, but we are saying that it isn't better.
Myth: Linux is faster than Windows
It's not true, but the focus is in the wrong place as the perceived speed of web sites is partly down to the operating system but mostly down to the Web Server Software than runs the sites.
For instance, the most common Web Server Software on Linux is Apache, but Litespeed is also available which is recognized to be several times faster than Apache for some configurations or installations. Windows 2012 comes with IIS8.0 as it's default web server and it is FAST - we mean REALLY fast. It's the best web server software Windows has ever produced and we think it's brilliant.
At the end of the day there's nothing in it. Server 2012 and IIS8 run PHP and MySQL extremely fast, but so do many Linux installations; some run them extremely poorly. At this point we have to say the server administrators and web site optimizations have probably got more to do with the perceived speed than whether your site runs on Windows or Linux.
Myth: Linux is cheaper than Windows
It's true that Linux is an open-source system and can be free, but not every distribution or version is free and not every installation is open-source either. But putting that aside, it's not much of an argument either. The only way to legally provide Windows hosting is via an agreement with Microsoft. The monthly cost of a Windows 2012 Server licence is not a great deal of money - less than the price of many hosting plans - and that amount of money isn't going to make a great deal of difference to a hosting company in the grand scheme of things. Open-source systems aren't better than closed operating systems, it's just a different way of approaching something, and with more and more Linux distributions becoming closed it's a changing world.
It could be argued that the "free" aspect of Linux attracts dubious characters to hosting since the start-up costs are so little, but we'd never be ungallant enough to agree with that - there are many excellent, honest, and reliable hosting companies using Linux. Some hosts charge the same for Windows or Linux hosting, and some charge different prices. If prices are different it's usually down to some other factor than the cost of a windows licence such as the software provided, the level of service, or the specification of the server or hosting plan.
There are often other factors at play when it comes to the pricing of hosting plans, but the cost of the Windows Licence is not likely to be a consideration.
Myth: Linux is for PHP, PERL and MySQL, Windows is for ASP.NET and MS SQL Server
If your developer told you that then it's time to find a new one, and if they're an employee then it's time to fire them (just kidding!). That argument was lost many years ago - with Server 2012 and IIS 8.0 it's not even remotely true - and anyone clinging to that sad myth needs to wake up to the new reality.
Server 2012 and IIS 8 run PHP, PERL, and MySQL super-super fast. PHP caching is built-in to IIS 8 and it makes PHP applications fly. IIS 8 even supports URL Rewrites, so there's nothing holding you back.
If Server 2012 and IIS 8.0's PHP and MySQL performance wasn't enough, Windows hosting also fully supports the ASP.NET framework, legacy ASP, and MS SQL Server. ASP.NET sites are amongst the fastest, most reliable, and most stable web sites around. Many are so efficient that they deal with massive visitor numbers and hits with surprisingly low impacts on the hosting server resources, giving a massive boost to performance and reliability. Linux doesn't support ASP or ASP.NET particularly well, or at all in many cases, and doesn't support MS SQL Server either.
The fact is, you have a greater choice of programming and scripting languages on a Windows server than you do on a Linux server.
So what should you choose, Windows or Linux?
It's really down to you and how you feel about the hosting company, it's hosting plans, the way it operates, and the services it offers - not all hosting companies are the same.
If you have an ASP.NET or ASP site that uses MS SQL server then you probably don't have a choice but to use a Windows Hosting company, but for sites built with PHP or PERL and using MySQL then it's your choice whether to choose a Windows or Linux hosting company.
You may select a Linux hosting company for your own personal reasons and we can't argue with your decision. As long as your decision isn't influenced by out-of-date and inaccurate information or biases then your decision will be the best one for you and we wish you well.