Molecular electronics seeks to build circuitry using organic components with at least one dimension in the nanoscale domain. Progress in the field has been inhibited by the difficulty in determining the energy levels of molecules after being perturbed by interactions with the conducting contacts. We measured the photocurrent spectra for large-area aliphatic and aromatic molecular tunnel junctions with partially transparent copper top contacts. Where no molecular absorption takes place, the photocurrent is dominated by internal photoemission, which exhibits energy thresholds corresponding to interfacial transport barriers, enabling their direct measurement in a functioning junction.