The way that I look at it, Unix and Windows are both screwdrivers. One is phillips head, the other is a flat head. They do essentially the same thing in a slightly different way. When I have customers trying to make a platform decision I tell them that they're looking at the wrong thing. You do not determine a platform for your company's computing needs and then select applications for it. You decide what kind of functionality you need, then find the applications that best fit your need, and then you run the platform that they are supported on.
Depending on what you need to run there are advantages and disadvantages to every platform. Not being a Unix guru I couldn't tell you about everything. What I can tell you is that generally it is much less expensive to run Windows on commodity server hardware than it is to run one of the commercial Unix flavors. And that's just hardware and software licensing costs. Unix engineers and administrators are also a little harder to come by, and because they are viewed as being more niche they also tend to be better compensated than an engineer or admin on the Windows side. So your staffing costs would potentially be higher. Finally, because those skillsets are less common, finding qualified staffers to manage Unix-based infrastructures can be more difficult.
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CompTIA A+, Network+, Server+, Security+
MCTS:Windows 7
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