The scientific method
"On the ground, research rarely looks like the model of the scientific method presented in the textbooks."
Preaching to the choir! Ha! I rarely see how many of the core philosophy of science concepts, like the difference between induction and deduction, help when figuring out what an IR spectrum is telling you. Well, I suppose it does if you get into the highly abstract, but in actual research it's pretty useless.
Well, deduction and induction are logical concepts, not based in philosophy of science per se, although the latter makes heavy use of them. I think many of the more specialized areas of phil of sci can be useful to primary research though -- for example, work by philosophers of biology on units/levels of selection.