I discuss several novel phenomenological features of QCD which are observable in deep inelastic lepton-nucleon and lepton-nucleus scattering. Initial- and final-state interactions from gluon exchange, normally neglected in the parton model, have a profound effect on QCD hard-scattering reactions, leading to leading-twist single-spin asymmetries, the diffractive contribution to deep inelastic scattering, and the breakdown of the pQCD Lam-Tung relation in Drell-Yan reactions. Leading-twist diffractive processes in turn lead to nuclear shadowing and non-universal antishadowing--physics not incorporated in the light-front wavefunctions of the nucleus computed in isolation.