I'm a linux person, so take these remarks with a grain of salt.
I agree with both of the above posters. You'll find that you will need to engage your brain before working with linux, and that isn't a good thing for some people. This is both a blessing and a curse. I find that in linux, there are a variety of tasks which would take delving through assorted dialog boxes taking very little time comparativly on the command line. Because I've always been a keyboard person, I have a tendancy to like the command line more than a GUI, though, when one is well designed I will use it.
On a server, I think you will need to think about a couple of things. First: Do your people have experiance. Linux is getting easier and easier to use, but it's amazingly helpful to have a wizzard hanging around to back you up.
Second: What is this thing to be doing? If it's doing something minor, like serving small numbers of files to an small-medium internal network, then perhaps it may be better to stick with windows. It's probably easier to maintain on a smaller level. On a larger network, or where you are seeing mission critical applications, then linux may be a better way to go. It has a history of being reliable, and on a bigger scale, easier to administer. The command line paired with SSH means you can administrate any machine from anywhere, with minor setup tweaks. A linux network at the large size, and in clusters, is nice to just sort of set it and forget it.
Third: Hardware. Is the hardware, for a large setup, fairly homogenous? If not, you could run into issues with support, and an administration overhead. If it is homogeneous, then you could conceiveably set up a master image, roll it out to everything, and then tweak the boxes as needed. <edit>fourth, What about support? Are you buying into a vendor, like RH? If not, then you are lacking a security net that is probably prudent. If you know your network like the back of your hand, then perhaps you don't need the net, but hey, better safe than sorry.</edit>
I think, as linux v. windows always does, it all comes down to Simplicity versus power.
I didn't adress security here, because it becomes a sort of religious thing. Depending on who you trust, either linux or windows is more secure. Of course, the most secure OS (out of the box) is OpenBSD.