Actually the choice of OS for the server depends on several points:
1. What technology you use - sure, if you use ASP language or if you plan to use MS SQL database then Windows OS is required.
2. If you plan to manage your account yourself, then the choice also depends on your technical skills - if you have appropriate ones, i would prefer Unix OS since it is easier to manage the account settings as well as remotely it is managed much better than Windows OS.
3. Unix plans are cheaper
Anyway, i would not use Windows OS until it is the only possible alternative .
As for our company, we advise our customers (who build e-commerce sites) to use Unix/Linus based servers.
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