windows hosting must be only used for special kind of applications like asp.net , or for a data base company,
While I prefer linux or shared hosting as its a good way to host a website, I prefer it in most of the cases.
I agree with tsak. linux is vastly more robust and stable. However, windows is entirely more user friendly for the techie who simply doesn't know linux yet. Personally I don't know LINUX yet, but im learning and not confident enough to begin using them in deployment boxes. Windows is rather simple to use but like others have stated before i has many holes in it. As far as windows itself being unstable I have not had any random crashes from windows server 2008 r2 so I can't speak for 2k3.
With Cpanel's enkompass now being a free product it makes it rather easy to get started using windows servers with the major cost being the operating system itself which is rather pricey. Support for windows boxes is frustrating as well with it being microsoft. Installing plesk on a windows box proved to have some challenges with it but Cpanel's Enkompass has exhibited some odd behavior too. All in all though I am more than happy and can see Windows as a viable and scalable solution provided they continue to pour themselves into its development. Hope this helps someone.
Right now if you know linux I would reccomend going with a linux OS.