I've run both - and there's pluses and minuses to each. It used to be that the big advantage to Windows was driver support, but they're much closer these days. Maintaining a bunch of machines is much easier if it's linux (IMO), and it tends to be much more light-weight in terms of disk size and memory footprint. The biggest plus I think with Linux is a bit of a one-time thing, but I can have a new system up and mining from the same image, even if I change motherboards, etc - I have 3 classes of machines in my mine, and they all run the same Linux image. With Windows you need a different one for each machine, and on system you have to wait for it to detect all the cards, which depending on how many you have can take a while.
That being said, if you're more comfortable with Windows then do it - there's also more 'exotic' things for Windows, like better profit-switching software, etc. But then on the Linux side you have about a bunch of different custom miner OS versions and even more forks.
In the end it's Linux for me - just easier to deal with, but I also run my own OS image, I don't run any of the ones others have released, although I've played with them.
You probably have a very big skill in Linux, I never used Linux until the moment when I did not know that using the optiminer program for Linux, I can mine up to 10 times more (I'm not kidding). This was the decisive argument and I installed Linux ubuntu, though I still figured out how to run the optiminer program with the system startup.
