1. King's Field (1996)
2. Chrono Trigger
3. Final Fantasy IX
4. Baldur's Gate: Dark Alliance
5. Final Fantasy VI
6. Final Fantasy VIII
7. Opoona
8. Final Fantasy VII
9. Crystalis (NES version)
One of the best games on the NES, period. Done in the original Legend of Zelda style, but with added RPG-elements, better graphics, more enemy variety and location variety, and more NPCs and towns to interact in. I've wanted a sequel to this so badly, for so long. But shortly after this is when SNK began to focus on arcade games a lot more, especially fighting games.
I'm just not the biggest Final Fantasy fan, myself. I like RPGs and have played some of them to try to get into them, but they just don't grab me. I've finished 1, 2, 9, and Mystic Quest. And I've tried 4, 6, and 7.