Brain functional connectivity can be characterized by the temporal evolution of correlation between signals recorded from spatially-distributed regions. It is aimed at explaining how different brain areas interact within networks involved during normal (as in cognitive tasks) or pathological (as in epilepsy) situations. Numerous techniques were introduced for assessing this connectivity. Recently, some efforts were made to compare methods performances but mainly qualitatively and for a special application. In this paper, we go further and propose a comprehensive comparison of different classes of methods (linear and nonlinear regressions, phase synchronization, and generalized synchronization) based on various simulation models. For this purpose, quantitative criteria are used: in addition to mean square error under null hypothesis (independence between two signals) and mean variance computed over all values of coupling degree in each model, we provide a criterion for comparing performances. Results show that the performances of the compared methods are highly dependent on the hypothesis regarding the underlying model for the generation of the signals. Moreover, none of them outperforms the others in all cases and the performance hierarchy is model dependent.