At the end of the day, running multiple applications, dealing with various types of multimedia, and running your site with a certain infrastructure make a large impact in how your website is run and maintained. Among some of the limiting features of Windows hosting are that if you want to run a Microsoft website you'll have to use Windows hosting. If you are running a Microsoft website you are also going to have to use a Microsoft database like SQL Server. While SQL Server is robust and reliable, it has a large learning curve, so you better have experienced database administrators to run your website. While this may be the case, some of the benefits that Windows platforms are known for are their high level of interactivity and easy access to the database for the programmer.

If you are not dealing with such a robust database like SQL Server, some webmasters would even say that Windows hosting is easier to handle than Linux hosting. One of the downsides though, is that if you start off hosting your website under a Windows platform and then decide to make the conversion to a Linux server, the transition is going to be next to impossible. That being said, it's not exactly any easier to make the conversion the other way either. Bottom line, the platform that you decide on should be the platform that you end up using for the long run.

Some features that Linux is known for is its stability and reliability. This means that customers with websites hosted on Linux servers will have little need to worry about website security. This is a great deal of pressure off of your shoulders, especially if you're running an e-commerce website or one that values private information. Obviously, this is something that every customer is looking for. It's not like Linux is lacking in terms of interactivity either.

Basically, unless you know that you will be using many Windows-based applications, Linux offers more overall flexibility in the event that you alter the direction of your website.