Sonic (If not for ADX and A2B this wouldn't make top 3)
Fire Emblem
Tales of _______
Though honorable mentions to Zelda, New Spyro, Smash Bros, Pokemon, and some smaller games I've played such as Summon Night Swordcraft Story, Golden Sun or Harvest Moon. Ah I play too many games to have a favoite but generally the ones I like most are those top 3.