Photocurrents generated by illumination of carbon-based molecular junctions were investigated as diagnostics of how molecular structure and orbital energies control electronic behavior. Oligomers of eight aromatic molecules covalently bonded to an electron-beam deposited carbon surface were formed by electrochemical reduction of diazonium reagents, with layer thicknesses in the range of 5-12 nm. Illumination through either the top or bottom partially transparent electrodes produced both an open circuit potential (OCP) and a photocurrent (PC), and the polarity and spectrum of the photocurrent depended directly on the relative positions of the frontier orbitals and the electrode Fermi level (EF). Electron donors with relatively high HOMO energies yielded positive OCP and PC, and electron acceptors with LUMO energies closer to EF than the HOMO energy produced negative OCP and PC. In all cases, the PC spectrum and the absorption spectrum of the oligomer in the molecular junction had very similar shapes and wavelength maxima. Asymmetry of electronic coupling at the top and bottom electrodes due to differences in bonding and contact area cause an internal potential gradient which controls PC and OCP polarities. The results provide a direct indication of which orbital energies are closest to EF and also indicate that transport in molecular junctions thicker than 5 nm is controlled by the difference in energy of the HOMO and LUMO orbitals.