I've built a number of websites and other apps that required .net and all have had problems - always the fault of some .net quirk or .net upgrade. I still run both linux and MS web services. By far the most reliable, economical, and feature intensive are the linux systems. The open source community is kicking butt! Maybe that's why MS is looking at joining. I work on mostly Windows systems, but I had an Ironport MTA appliance running a *nix derivative of some kind, and a quirk in the regex implementation of the Java version it was running drove me freaking nuts for 2 days.
I didn’t mention Java up thread for a reason. ;-) How many routers, switches, firewalls, NAS, ..., have MS as an OS?