The scanning tunneling microscope is a versatile tool to study nanoscale structures with atomic resolution through a combination of manipulation and spectroscopic capabilities. By a process of inelastic scattering, tunneling electrons can probe vibrational, configuration and spin-flip excitations with single-atom sensitivity at low temperatures (T less than 5K). I will discuss examples where inelastic electron tunneling spectroscopy (IETS) has been applied to build isotope-selected molecule cascades, study two-state dynamics of molecular hydrogen, and probe magnetic spin-flip energies of single manganese atoms. Molecule cascades are precise arrangements of carbon monoxide molecules in which the motion of one molecule induces a cascade of motion similar to a row of dominos. Quantum tunneling of CO molecules in the cascade has been established by measuring propagation rates as a function of temperature and molecular weight. Isotope-selected molecule cascades were built by using IETS to measure isotopic shifts of the frustrated rotation mode of CO on a Cu(111) surface. Molecular hydrogen adsorbed on surfaces can exhibit a variety of phase transitions that are distinctly different than the bulk. We have discovered strongly coverage-dependent excitations of molecular hydrogen adsorbed on metal surfaces at low temperature (T=5K). These excitations appear as pronounced nonlinearities in tunneling spectra which produce both negative differential resistance and gap-like features. The lineshapes of these nonlinearities can be understood with a simple saturation model for a two-state system. Transitions between these states are driven by inelastic scattering of tunneling electrons. The onset of the nonlinear spectra at a threshold coverage (less than 1 monolayer) is suggestive of a phase transition. The spectral resolution in IETS is limited by thermal smearing of the Fermi-Dirac distribution of tunneling electron energies. In order to study low-energy magnetic excitations, a novel He-3 STM was recently constructed that operates at temperatures down to 0.5K with a magnetic field up to 7T. Using this instrument, we were able to study the Zeeman spin-flip energies of single Mn atoms on an NiAl:Al2O3 surface. The oxide surface was employed to decouple the Mn atoms from surface conduction electrons. A variety of local metal-oxide environments were found to influence the magnetic signatures of Mn atoms in spin-flip IETS.