Using the selected ion flow tube technique, the rate coefficients and reaction pathways have been obtained at 300 K for the reactions of Ne+ and Ne+2 with a variety of molecules including NO, O2, CO, H2, N2, OCS, N2O, CO2, NO2, H2S, SO2, NH3, C2H2, CH4, C2H4, C2H6, C3H8 and n-C4H10. During the course of this work the rate coefficients for the reactions of HeNe+ with these molecules were also obtained and are therefore presented in this report. The majority of reactions proceed via non-dissociative and/or dissociative thermal energy charge transfer processes. Using available photoelectron spectra, the influences of energy resonances and Franck-Condon factors on the efficiency of these processes are examined. There are indications that for many of the reactions distortions of the Franck-Condon factors occur leading to more efficient reactions than would otherwise be expected. Evidence for the importance of electron correlation effects during thermal energy charge transfer is presented. This should have far reaching implications outside of this study.