Crooked Timber blogs about Charles Stross' "A Colder War". I read this a few years ago when it featured in a Dozois Year's Best anthology, and it grabbed me immediately. It starts out ordinarily enough - just a soulless CIA analyst looking at some files - and then before you know it you're down the rabbit hole and reading about shoggoth gaps and an exchange of weakly godlike entities. It has everything - Auschwitz, Chernobyl, Oliver North and Stephen J Gould; a fantastic cross between the Mythos and the Cold War.
Like many, I was struck by the similarities between Stross' vision and Delta Green - except that it seems too overt. The world of Delta Green is supposed to be indistinguishable from our own; the horror is hidden behind the curtain, glimpsed out of the corner of the eye (or, if you're unlucky enough, it swallows you whole in the middle of the night). Having shoggoths paraded through Red Square like SS-20s, or nameless horrors imprisoned under the Pentagon as a final deterrent (a more insane form of MAD) would spoil that aspect. Besides, no-one in Delta Green would be mad enough to see the Mythos as a weapon... would they?