  In this thesis we explore a diverse array of issues that strike at the
inherently nonperturbative structure of hadrons at momenta below the QCD
confinement scale. In so doing, we mainly seek a better control over the
partonic substructure of strongly-interacting matter, especially as this
relates to the nonperturbative effects that both motivate and complicate
experiments --- particularly DIS; among others, such considerations entail
sub-leading corrections in $Q^2$, dynamical higher twist effects, and hadron
mass corrections. We also present novel calculations of several examples of
flavor symmetry violation, which also originates in the long-distance
properties of QCD at low energy. Moreover, we outline a recently developed
model, framed as a hadronic effective theory amenable to QCD global analysis,
which provides new insights into the possibility of nonperturbative heavy
quarks in the nucleon. This model can be extended to the scale of the lighter
mesons, and we assess the accessibility of the structure function of the
interacting pion in the resulting framework.
