Surface effects significantly influence the functionality of semiconductor nanocrystals (NC). A theoretical understanding of these effects requires an atomic-scale description of the NC surface. We present an atomistic tight-binding theory of the electronic and optical properties of partially passivated cadmium sulfide NCs. Fully passivated quantum dots, with all dangling bonds saturated, have no surface states in the fundamental band gap. When all surface anion dangling bonds are unpassivated, two anion-derived, surface state bands lie above the valence band edge. By investigating NCs with a single unpassivated surface anion, we are able to assign the surface state bands to states derived from surface anions with one or two unpassivated dangling bonds. The surface state energies for a NC with a single unpassivated surface S atom depend of the number of unpassivated dangling bonds, but are not otherwise strongly sensitive to the local atomic environment. Unpassivated surface dangling bonds can also shift the internally confined states, split their level degeneracies, break their symmetry and change their oscillator strengths. For NCs with multiple unpassivated surface S atoms, coupling between unpassivated dangling bonds can occur across the entire NC, leading to substantial mixing of dangling bond states and significant broadening of the density of states. Ordered rings of unpassivated dangling bonds show level coupling analogous to coupling in molecular rings. The surface states of clusters of unpassivated anions depend on the cluster size. The optical response due to internally confined states becomes indistinguishable in the broadened optical response as the cluster size increases. Incomplete surface passivation is modeled by considering NCs with randomly passivated surface atoms. For a low density of unpassivated surface anions, the density of surface states broadens substantially as the density of unpassivated surface anions increases. The fundamental NC optical response due to confined states disappears if 30 percent of the S surface atoms are unpassivated. However, at a high density of unpassivated surface anions, the density of surface states narrows as the density of unpassivated surface anions increases and NC evolves to a more ordered structure with all surface atoms unpassivated. Comparable effects are found for NCs with unpassivated surface cations. The coupling between anion-derived and cation-derived surface states is weak because these states occur at very different energies.