We compare the density functional theory (DFT) results on the adsorption of small aromatic molecules (benzene, pyridine and thiophene) on gold surfaces obtained by using three types of van der Waals exchange-correlation functionals and localized basis set calculations. We show that the value of the molecule-surface binding energy depends on the interplay between the BSSE effect and the tendency of the exchange-correlation functionals to overestimate both the molecule-surface as well as the gold-gold distances within the relaxed systems. Consequently, we find that by using different types of LCAO basis sets or geometric models for the adsorption of the molecules on the surface, the binding energy can vary up to 100 %. A critical analysis of the physical parameters resulting from the calculations is presented for each exchange-correlation functional.