This Minireview gives an overview of recent progress in the design and analysis of chemical systems that utilize template-directed autocatalytic and cross-catalytic processes as a means of wiring dynamically interacting molecules. Synthetic networks comprising two to nine replicating species are discussed. It is shown that for larger systems, more catalytic pathways must be manipulated to control the entire network topology and specific functionality of the individual species or subnetworks. Cellular biochemistry is an example of a natural functional molecular network; synthetic self-organized networks can provide additional models of complex systems.