The quantum-chemical perspective may be illuminating:
Within QC, nuclei are typically modeled as being wholly classical or semi-classical.
For the dynamics of hydrogen transfer in some situations, the effect of proton tunneling can be measured, but even then it can be regarded more as a correction to the classical behavior. For heaver elements (Z > Be or so) I don't even think it's measurable in 'ordinary' circumstances. Obviously you have BECs, and double-slit diffraction has been measured for C60, but the former is a rather extreme circumstance and the latter effect isn't enough to be chemically significant.
So all electronic and chemical properties of an atom/molecule (bonding, ionization potentials, etc) all radiation/matter interactions, intermolecular energy transfer of other sorts, all electron kinetics, and some proton kinetics are quantum-mechanical. Vibrational and rotational energy levels are well treated semi-classically. Molecular structure, large scale molecular motion/diffusion, chemical reaction rates etc are classical.
For instance, the relative energies of chemical compounds and 'activated complexes' (in transition-state theory) are entirely quantum-mechanical in their origin. But the resulting equilibria and reaction rates are well-described with classical statistical themodynamics once you know the energies.
Ask me what the vibrational energy levels of a molecule are, and I have to use QM to some extent to get the answer, even if it means a simplified harmonic-oscillator or Morse potential (i.e. a semi-classical description is fine as long as I can ignore vibronic coupling, in other words, as long as the electrons don't get involved too much). But the distribution of the vibrational levels in a system? Classical stat-mech. The origin of the vibrational potential-well? Quantum mechanical.
In short it all meshes together nicely. You don't just stop using QM at one level and switch to classical (or vice versa), there's a range of semi-classical models that bridge the gap.