Yale/Stanford: the extra stuff matters a bit more than any other schools. At least that's the reputation they have.
The other 3 of the top 5 is primarily a numbers game.
It might also help to know which school we're talking about here. If it's Stanford, well, that's one thing. If it's Emory, that's wholly another. And numbers would help—plus years of WE, diversity factors (first gen grad, etc.).
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They do overlap (http://plato.stanford.edu/entries/logic-classical/#1 ... application in math (http://plato.stanford.edu/search/searcher.py?query ... math is logic (http://plato.stanford.edu/entries/philosophy-mathematics/#Log)