know the recommended courses to take that will be of interest to an applied mathematician.
What do you want to do? Obviously you should concentrate on that.
Almost anything in physics is probably of some interest. In CS, see Bourbaki's post, and statistics / advanced probability are great things to know.
Other than that, there are various computational aspects of the sciences. Anything training you in simulations is probably a nice thing - you can find that in operations research classes, finance, all sorts of things.
Knowing programming is not strictly applied mathematics, but really helps for applied mathematics endeavors.
I'd say more than specific knowledge, you should develop an interest for using certain kinds of thinking, because the nature of applied mathematics is that it can be very broad.
Familiarity with simulations, knowledge of advanced statistics, probability, differential equations, and knowledge of programming, together with a basic undergraduate math foundation should prepare you to specialize in almost anything. Oh and you should be comfortable with Fourier transforms for sure.