Jason Kottke compares the unix philosophy and the Microsoft one:

If Unix development philosophy is small pieces loosely joined, Microsoft's philosophy is big chunks tightly coupled.

Jason uses three words to describe how Microsoft keeps its developers: Friction, Inertia, and Marketing. FIM. I'm not saying that Microsft does not make some amazing products (not including Windows, at least to-date) but that (and this is from experience) it's an uphill battle to mix unix- and Windows-based applications in an environment, because the design philosophies are so different.

Microsoft [server] apps are designed to work with each other. Period.