There are a number of published works in which small molecules are used to control the fate of embryonic stem cells, including self-renewal and differentiation toward specific cell lineages (e.g., subtype specific neurons, cardiomyocytes). Those chemical compounds were either discovered from cell-based phenotypic screens or specifically selected based on hypotheses derived from knowledge of developmental signaling mechanisms. For more and detailed examples, people can read  Nature (2008) 453, 338-44 .