Relative surface topography of metal electrodes is one of the subtle issues determining the electrical performance of molecular devices. Systematic conductivity measurements of nanoscale junctions containing self-assembled monolayer of conjugated molecules are reported for a variety of metal electrodes. The monolayer is assembled on 25-100 nm electrode. Another 10-100 nm electrode is defined on top of the monolayer by metal evaporation. The characteristic energy scales are determined from the temperature dependence of conductance and from the non-linear current-voltage characteristics. Unexpectedly, the energy scales of the dominant conductance channels are small in comparison with the molecular level spacing. In all cases, the dominant room temperature conductance is hopping with characteristic energy of the order of 10-100 meV determined by the nature of metal contacts. Relative contribution of tunneling conductance strongly depends on the surface topography of the metal electrodes.