The ‘cone kinetics’ model, which explains development of cone-shaped inclusions during nanocrystalline silicon film growth and during low-temperature silicon epitaxy breakdown, is extended to protocrystalline (‘edge’) amorphous silicon, Si heterojunctions and other Si film morpholologies. We generalize the physics underlying cone formation and present diagrams that delineate the deposition regimes giving rise to the different film morphologies; these regimes are determined by the nucleation rate of the second phase and the relative growth rate of the phases present. The model predicts cone growth during thin-film deposition by plasma-enhanced and other chemical vapor deposition techniques when isotropic growth is coupled with the isolated nucleation of a second phase with a higher growth rate. Protocrystalline amorphous silicon and other embedded crystallite phases are formed when a second phase successfully nucleates but has a smaller growth rate than the surrounding amorphous film. The cone kinetics phase diagram provides a simple explanation of the various nanocrystalline film morphologies observed when silane precursors are diluted with different concentrations of hydrogen gas.