We compare the accuracy, precision, and reliability of different methods for estimating key system parameters for two-level systems subject to Hamiltonian evolution and decoherence. It is demonstrated that the use of Bayesian modeling and maximum likelihood estimation is superior to common techniques based on Fourier analysis. Even for simple two-parameter estimation problems, the Bayesian approach yields higher accuracy and precision for the parameter estimates obtained. It requires less data, is more flexible in dealing with different model systems, can deal better with uncertainty in initial conditions and measurements, and enables adaptive refinement of the estimates. The comparison results show that this holds for measurements of large ensembles of spins and atoms limited by Gaussian noise as well as projection noise limited data from repeated single-shot measurements of a single quantum device.