Windows and UNIX are in fact two different systems and of course we are referring to computer systems. A web host uses computers, (we shall refer to them as servers, just computers, but sometimes larger) to host websites, and all computers need a operating system, so Windows and UNIX are the operating system.
The Windows used is normally Windows NT or 2000 and of course as you know Microsoft charges for it’s software, while UNIX is an open source operating system, this means that the original creators of the system have given up the rights and anyone can use it, change, improve or do anything they want with, free of charge.