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When <pick your favorite application> is part of the OS there is a serious problem.
This has been MS's problem all along - throw all the app garbage in the OS to create a faster, flashier app with the downside of breaking all known design principles not even to mention the anti-trust implications.
They lived by that sword and now they are dying by the same sword. In the 90's they won the browser and desktop wars by loading up the OS with application code. Now they're paying for it in the 2000's by having a unwieldy, unmaintainable "kernel" which is not even a kernel at all but a collection of apps, display managers, window managers, wizards and the like.
Vista may be their Waterloo. It's looking like that now, at least to me.
I see you meant Spam Filtering as an example to prove a more general point - you and I are in complete agreement.
Because of things like this ("SPAM filtering is part of the OS") Windows should be considered an Operating Environment, because it goes way beyond the traditional bounds of an operating system. The OS should be a layer on top of which one could build a GUI. That is how X works, running on top of the Linux kernel.