I can agree with Dragon Warrior IV. I missed out on the NES era so I decided to pick up the console a few years ago, and Dragon Warrior (Quest) IV was the first game I bought for it. I love the way how each character is introduced and given their own little story before they meet up with main character. Mother (Earthbound Beginnings) is another JRPG that I loved despite some really annoying issues.
Most of my others favorites are all fan-translated games, lol. Fire Emblem Gaiden, Famicom Wars, Final Fantasy III just to name a few.
And of course, can't forget about Super Mario Bros. 3