A fundamental understanding of quantum chromodynamics, particularly at the amplitude level, is essential for progress in high energy physics. For example, the measurement and interpretation of the basic parameters of the electroweak theory and CP violation depends on an understanding of the dynamics and phase structure of exclusive B-meson decay amplitudes. In this review, I discuss a number of ways in which the required hadron wave-functions can be measured (such as two-photon reactions and diffractive dissociation) or calculated from first principles. An important tool for describing relativistic composite systems in quantum field theory is the light-front Fock expansion, which encodes the properties of a hadrons in terms of a set of frame-independent n-particle wavefunctions. Light-front quantization in the doubly-transverse light-cone gauge has a number of remarkable advantages, including explicit unitarity, the absence of ghost degrees of freedom, and the decoupling properties needed to prove factorization theorems in high momentum transfer inclusive and exclusive reactions. Evolution in light-cone time allows the construction of an ''event amplitude generator'' in which only non-ghost physical degrees of freedom and integration over physical phase appear. The diffractive dissociation of a hadron at high energies, by either Coulomb or Pomeron exchange, has a natural description inmore » QCD as the materialization of the projectile's light-cone wavefunctions; in particular, the diffractive dissociation of a meson, baryon, or photon into high transverse momentum jets measures the shape and other features of the projectile's distribution amplitude. Diffractive dissociation can thus test fundamental properties of QCD, including color transparency and intrinsic charm. I also review recent work which shows that the structure functions measured in deep inelastic lepton scattering are affected by final-state rescattering, thus modifying their connection with the light-cone probability distributions. In particular, the shadowing of nuclear structure functions is due to destructive interference effects from leading-twist diffraction of the virtual photon, physics not included in the nuclear light-cone wavefunctions.« less