Calling my dad lets me save my game and lets me know how much money is in my bank account. Calling my mom didn't seem to do much of anything. Why should I bother calling her?
Ness can suffer from an ailment called Homesick by not talking to his mother for long periods of time. When he has this status condition he can sometimes miss turns in battle.
Calling your mother will prevent Ness from becoming homesick and it will also cure the homesick ailment! Silly moms.