Ohhhh no, here we go.....I really am not sure that I want to get involved in the eternal debate, however I am going to have to disagree with John Hoke.
I would have to say that for the most part linux is more secure, however that is swaying slightly to Microsoft's favor. Historicly, Linux has always been a computer geeks OS. Now that the Linux community is trying to shake this image and open the market up to the average desktop it's going to lose hold of that (in my opinion).
Microsoft caters to the masses, and the reality is that when it comes to high level administration the masses simply don't know. I mean what does the average person care about ACLs, SIDs, SAM, etc... So you have inexperienced people deciding that it would be cool to throw up a web and e-mail server. Now you have a ton of boxes out there that are never updated and where never secured to begin with and all of a sudden Microsoft products have a bad name. I would put any properly administered NT/2000 box up against any equally administered Linux box.
Now that was the server end. Now on the desktop, each platform has it's own pluses and minuses. However, Windows has the distinct advantages of user base, brand recognition, and corporate accountability. Linux and the open source community can't offer that.
I can't say that one is better than the other, but the bottom line to me is that Windows is the standard that the business world follows. And it's not just Windows either, it's MS Office, Exchange, Word Perfect, and about a million other products that have a corporation standing behind them. People know how to use these products, have the features that they know and use. That may change in coming years, but it doesn't change where we are at right now. Linux needs to develop some solutions for the business end user and then the heat may be turned up a bit. Right now, Microsoft has the advantage and so sorry to tell you but they are not going to lie down and go away.