In this paper we give five gauge-invariant systems of governing equations for first and second order scalar perturbations of flat Friedmann-Lemaitre universes that are minimal in the sense that they contain no redundant equations or variables. We normalize the variables so that they are dimensionless, which leads to systems of equations that are simple and ready-to-use. We compare the properties and utility of the different systems. For example, they serve as a starting point for finding explicit solutions for two benchmark problems in cosmological perturbation theory at second order: adiabatic perturbations in the superhorizon regime (the long wavelength limit) and perturbations of ACDM universes. However, our framework has much wider applicability and serves as a reference for future work in the field.