Annihilation, of course. If I can produce at will the element I've chosen, I'll have the most powerful energy source and explosive in existence. Hmm, maybe I should go with antideuterium instead, so that I have protons, neutrons, and electrons all covered. But then again, I can always make neutrons by forcing the electron and proton inside a hydrogen atom to undergo reverse beta decay, if my control extends that far.
If we cannot create the element we control, and can only control already existing atoms of the element, then the obvious choice would be carbon or hydrogen or some other common element. And that's boring.