Scanning tunneling microscopy (STM) has been used to investigate the influence of different substrates on monolayer ordering and molecular image contrast for singly and doubly substituted long-chain hydrocarbons. Self-assembly at the phenyloctane-graphite and phenyloctane-MoS2 interfaces can be mildly or strongly affected by the underlying surface. In the most extreme cases, changes in the ordering of two-dimensional adlayers involve both rotation and translation of the molecules. Differences in the electronic characteristics of the underlying surface also have important implications for the STM image contrast exhibited by many molecules. Careful inspection of functional group contrast on both substrates provides useful information about the relative importance of geometric/topological versus electronic coupling factors in the STM tunneling mechanism for physisorbed molecules.