The realization of molecular-scale electronic devices will require the development of novel strategies for controlling electrical properties of metal/molecule/metal junctions, down to the single molecule level. Here, we show that it is possible to exert chemical control over the formation of metal/molecule...molecule/metal junctions in which the molecules interact by pi-stacking. The tip of an STM is used to form one contact, and the substrate the other; the molecules are conjugated oligophenyleneethynylenes (OPEs). Supramolecular pi-pi interactions allow current to flow through the junction, but not if bulky tert-butyl substituents on the phenyl rings prevent such interactions. For the first time, we find evidence that pi-stacked junctions can form even for OPEs with two thiol contacts. Furthermore, we find evidence for metal|molecule|metal junctions involving oligophenyleneethynylene monothiols, in which the second contact must be formed by the interaction of the pi-electrons of the terminal phenyl ring with the metal surface.