We consider some of the issues surrounding the formation and evolution of Q-balls in the MSSM and its extensions. The ratio of the baryon number packed into Q-balls to that outside, fB, plays a fundamental role in determining the relationship of dark matter to the baryon number in the Universe at present. The final value of fB will depend upon the details of the formation of Q-balls from the collapse of the Affleck-Dine condensate and upon the subsequent evolution of the ensemble of Q-balls. We discuss the implications for neutralino dark matter in the gravity-mediated scenario and show that a light neutralino is necessary in most cases to account for the baryon to dark matter ratio, with an NMSSM singlino LSP of mass mχ20 GeV being a favoured candidate.