During the past decade we have looked at several ways to track the distribution of unpaired electrons during chemical reactions and in different spin states. These methods were inspired by our previous work on singlet di-radicals where the spin density is zero yet there are clearly singly occupied orbitals. More recently we have been concerned with analysis of wave functions for single molecule magnets. This review discusses the mathematical framework by which open-shell systems can be described, in addition to methods that extract the effectively unpaired electron density, the spin state of atoms in a molecule, and other useful properties from a molecular wave function. Some of the difficulties associated with using broken spin Slater determinants to evaluate the exchange coupling parameters in the Heisenberg Hamiltonian are also mentioned.