Linux or Windows?
The vast majority of us use Microsoft Windows on our desktops. This has been true for many years now. So the obvious answer to this could be 'we'll use windows because we're familiar with it'.
The truth is you never really see your webserver. You are only ever likely to connect to it through your web browser (Internet explorer) or email client (outlook etc). So your server being Windows or Linux doesn't matter from this point of view.
What does matter is price and reliability and unfortunately from Windows point of view Linux wins both times. At Duo we know from experience how much quicker, reliable and cheaper a Linux system is. Linux unlike windows is open source, this mean most of the code is written free of charge by volunteers and universities. Free usually means not very good. But in webhosting the free software often outperforms the expensive Microsoft equivalent. In three years of hosting websites we have never had a website go offline due to Linux failing.
We're not alone in believing Linux and their Apache webserver are the best according to http://news.netcraft.com/ in 2004 68% of sites are run on Apache and only 22% are Microsoft.