First of all, only your website will have Linux or Windows platform. All your emails will be hosted in Linux platform for stability and scalability reason.

Linux is the prefered choice because it is more stable than Windows unless your website has to be constructed by Windows programming such as ASP, ASP.NET.

If you do not know whether your website will be using ASP / ASP.NET, I recommend you to choose Linux first. Later on, your website could be changed back to Windows. Additional charge may apply if your current plan does not have windows plan.

for detail: webdesign.about.com/od/webhostin ... _linux.htm