well the stability is a big factor. Not jus that, you get too configur a whole lot more. I mean, most windows users probably dont even know what a kernel IS, let alone what it does and how it works. In linux, you actually get too configure HOW your kernel works and what it does.
You see - in a way, no linux installation is the same. If you choose to bootstrap the source to your CPU, and emerge the entire system from scratch (it takes about 20-30 hours but what the hey!!) what you have is an os that has been built, from the ground up, to exactly match your hardware, and use everything to its full potential. You dont need to waste resources having your kernel do things that you dont even need!! Not too mention the shear power and control you have over everything that is happening in the environment. (also it is a hell of a lot more secure than windows. No need for Anti-virus in linux, cause it would be insanely hard to execute a virus in linux)
Of course i am just scratching the surface here. There are millions of reasons why linux is a better os than windows. im sure you could find some very good articles on this somewhere on the web.