This paper describes the ability of several ionic liquids cations for electroosmotic flow modulation in capillary electrophoresis. Organic salts based on phosphonium, sulfonium, cysteinium, ammonium, and guanidinium cations were selected to study this property. In addition, the synergistic effect of these compounds in cyclodextrin chiral separation was also evaluated. In comparison with most studied imidazolium-based ionic liquids, several of the cations studied, are stronger modifiers in terms of electroosmotic flow (EOF) modulation. Phosphonium-based compounds and tri-octyl methylammonium chloride ([Aliquat]Cl) had the strongest ability to reverse EOF both in acidic and in basic conditions and had the lowest EOF reversal concentrations in the presence of hydroxypropyl-β-cyclodextrin. EOF modulation ability of phosphonium cations also contributed to the improvement of chiral separation of DL-propranolol by hydroxypropyl-β-cyclodextrin at lower concentrations in comparison with most commonly used EOF modulators such as tetrabutylammonium phosphate.