Many of today's forefront materials, such as high-Tc superconductors, doped semiconductors, and colossal magnetoresistance materials, are structurally, chemically and/or electronically inhomogeneous at the nanoscale. Although inhomogeneity can degrade the utility of some materials, defects can also be advantageous. Quite generally, defects can serve as nanoscale probes and facilitate quasiparticle scattering used to extract otherwise inaccessible electronic properties. In superconductors, non-stoichiometric dopants are typically necessary to achieve a high transition temperature, while both structural and chemical defects are used to pin vortices and increase critical current. Scanning tunneling microscopy (STM) has proven to be an ideal technique for studying these processes at the atomic scale. In this perspective, we present an overview of STM studies on chemical disorder in unconventional superconductors, and discuss how dopants, impurities and adatoms may be used to probe, pin or enhance the intrinsic electronic properties of these materials.