Interaction energies and geometries for van der Waals (vdW) complexes from ab initio calculations must take into account limitations associated with basis set flexibility, electron correlation, and basis set superposition error (BSSE). Presented are a variety of nb initio calculations on the helium, neon, and methane homodimers and the helium-methane and neon-methane dimers. Systematic changes in polarization and diffuse functions, the treatment of electron correlation, and the influence of BSSE correction were undertaken as a function of interaction distance. Calculations on the helium and neon homodimers were compared with available empirical data. Analysis of the contribution of the BSSE correction using the function counterpoise method indicates increases in minimum energy interaction distance when BSSE corrections are included. The presence of diffuse functions minimize the magnitude of the BSSE. The present calculations lead to the selection of the MP3/6-311++G(3d,3p) without BSSE correction as an appropriate level of theory for the calculation of relative interaction energies and geometries for different orientations between either helium or neon and molecules. An exponent for an sp diffuse function on helium was determined as part of the present study.