This paper presents a systematic treatment of the linear theory of scalar gravitational perturbations in the synchronous gauge and the conformal Newtonian (or longitudinal) gauge. It differs from others in the literature in that we give, in both gauges, a complete discussion of all particle species that are relevant to any flat cold dark matter (CDM), hot dark matter (HDM), or CDM+HDM models (including a possible cosmological constant). The particles considered include CDM, baryons, photons, massless neutrinos, and massive neutrinos (an HDM candidate), where the CDM and baryons are treated as fluids while a detailed phase-space description is given to the photons and neutrinos. Particular care is applied to the massive neutrino component, which has been either ignored or approximated crudely in previous works. Isentropic initial conditions on super-horizon scales are derived. The coupled, linearized Boltzmann, Einstein and fluid equations that govern the evolution of the metric and density perturbations are then solved numerically in both gauges for the standard CDM model and two CDM+HDM models with neutrino mass densities $\onu=0.2$ and 0.3, assuming a scale-invariant, adiabatic spectrum of primordial fluctuations. We also give the full details of the cosmic microwave background anisotropy, and present the first accurate calculations of the angular power spectra in the two CDM+HDM models including photon polarization, higher neutrino multipole moments, and helium recombination. The numerical programs for both gauges are available at http://arcturus.mit.edu/cosmics/ .