The effect of basis set superposition error (BSSE) on Gaussian-2 and Gaussian-3 calculated alkali metal cation-ligand affinities has been studied. For these systems, we found that the standard Boys-Bernadi full counterpoise (CP) method often leads to correction terms that are physically incorrect. This problem may be rectified by using the geometry corrected counterpoise (GCP) method. The relationship between CP, GCP corrections, and deformation energy is discussed. In order to yield good agreement with existing experimental Li+ and Na+ ligand affinities, we recommend the adoption of either the G3 (with GCP correction) or the G2(MP2,SVP)-FC (without GCP correction) protocols. In the case of K+, the GCP correction is of negligible magnitude, and hence GCP corrections may be omitted in the G2(MP2,SVP)-ASC affinity calculations for these complexes.