The design of future molecular electronic devices requires a firm understanding of the conduction mechanisms that determine their electrical characteristics. Progress toward this goal has been hindered by complications in controlling the exact configuration and makeup of fabricated molecular junctions, thus limiting the availability of quantitative experimental data for developing cohesive theories to model and predict molecular transport. This article summarizes recent research aimed at developing well-controlled systems for comparing molecular conduction and vibrational spectra using crossed-wire and in-wire metal–molecule–metal junctions. Systematic variations in molecular structure and metal–molecule contacts show strong quantitative agreement in device properties, while spectroscopic data provide evidence that the properties are due to the molecular junction. Further investigations using these and other molecular junction test beds will provide the needed experimental data to advance fundamental understanding of molecular transport and facilitate future molecular electronics applications.