Nanowire metal-molecule-metal junctions containing dithoilated molecules of dodecane (C12), oligo(phenylene ethynylene) (OPE), and oligo(phenylene vinylene) (OPV) were prepared by replicating the pores of sub-40 nm diameter polycarbonate track etched membranes. Bottom Au-S or Pd-S contacts were made by potential-assisted molecule assembly onto the tips of the first segment of the electrochemically deposited nanowires. Top S-Ag or S-Pd contacts were formed by depositing Ag or Pd nanoparticles, which also served as a thin seed layer for electrodeposition of the second nanowire segment. Room-temperature current-voltage (I-V) measurements of individual nanowires show that the conductance of junctions formed with pi-conjugated oligomers are several orders of magnitude larger than the saturated alkanes, with the OPV junctions having the highest conductance. The molecular wire junction conductance was also found to be dependent on the metal contacts with symmetric Pd-Pd junctions yielding the best metal-molecule coupling and highest conductance.