Nanostructures are often distinguished by their large surface-to volume ratios that, upon integration into devices, can lead to a high density of nanoscale interfaces. The impact of these interfaces on device function is, in many cases, not yet well understood. In this talk, I will describe recent theoretical efforts, using first principles density functional theory and many body perturbation theory, towards fundamental understanding of interfacial electronic structure and its relationship to measured transport and spectroscopy at nanoscale metal-organic and organic-organic interfaces. Examples to be discussed are the conductance of amine and pyridine-linked molecular junctions; chemical contributions to surface enhanced Raman scattering for benzene thiol on gold; and, if time permits, preliminary work on charge separation and optical absorption processes for covalently-joined donor-acceptor organic systems.