What basis do we have for certainty in current scientific theories?

Given there is much past scientific belief that we now know NOT to be true, what basis do we have for the seemingly increasing certainty in our scientific beliefs held today being true? On the one hand, we prize Popperian falsifiability and yet still have a sense that we can be quite certain of some things scientifically. I am thinking less about approximations such as Newtonian mechanics (which, even in light of relativity or quantum mechanics, is still useful) and more like phlogiston theory or Aristotelean physics. See http://en.wikipedia.org/wiki/Obsolete_scientific_theory for a decent list.