1. Who your client base is e.g. if its public sector and they want whatever you're producing to be ported to their servers it would have to be Windows
2. What your developers code in - PHP for Linux or .NET for Windows
3. Cost - Linux is normally a cheaper platform from a development point of view because decent .NET developers are *generally* more expensive than decent PHP developers. There also seems to be quite a bit more out there in terms of solutions and support for PHP dev.
We code on both and the windows stuff we do is for councils and the projects involved are much much bigger than the Linux PHP stuff we do.