The Linux or Windows debate where web hosting is concerned is mainly applicable to technicians. For the end user, especially those on shared hosting arrangements, there will be little appreciable difference in the experience no matter which operating system is chosen.
Linux is an open source operating system which is a very popular option for servers. It offers excellent security, flexibility and can be obtained, legally, for no charge. Windows Server is Microsoft’s proprietary server software. It is also very popular, is compatible with all Microsoft technology and benefits from there being a large number of individuals who are specifically trained and certified in operating the software.
On a shared hosting account, the web host will usually allow the customer to choose one operating system or the other. For most users, this will mean nothing more than some of the directories having different names and slight differences in operation. Because most shared hosting plans are administered from pre-made web interfaces, the technical aspects generally won’t have much impact on the user.
For dedicated hosting, the differences are vast. A very experienced Windows technician may be completely lost on a Linux system and vice versa. Generally, decisions such as these are based on software compatibility. If a business uses server software that only runs on Windows, for instance, the choice is obvious. If the business, on the other hand, has an IT person who has vast experience with Apache server and Sendmail, Linux would be the best choice.